Preparation.
As for any drum, while you have the heads removed, give the bearing edges a wipe with a soft cloth, and the inside of the hoops, the inside of the drum, and even the lugs.

Some people like to give the bearing edges a once over with paraffin wax to help give the head a full clean contact with the bearing edge of the drum. A good bearing edge is essential for a good sound. A quality drum should already have a good bearing edge, but every little bit helps. If you're worried about the sound of a drum, even after new heads are put on, get a good drum shop/technician to have a look at the bearing edges - there might be some dips or raises that will destroy the sound of the drum.

It is a good idea with any drum to add lubrication to the lugs about every 2nd or 3rd head change. This will make tuning easier, stop the lugs and the lug mounts from rusting. Some people use Vaseline, grease, sewing machine oil, carbon based powder, or a spray on lubricant. Personal choice, but don't get something that will collect dust too easily, as this will seize things up.

Tuning - Batter head.
This method gives the kick drum a punchy sound, an evenly tuned head, and best of all it's so simple it's a 3 minute job. If you prefer your drum to have more high end for whatever reason, follow these steps, then turn all the lugs the same amount (like an extra 1/2 turn or more) till you have the pitch you are after.

Place the head on the drum, place the hoop on the head, put each lug in. Finger tighten each lug, working your way around the drum in a star pattern, never from one lug to its neighbour. Tighten the lug at 12 O'clock, then the one at 6 O'clock, then the one at 3 O'clock, then 9, etc. I call it a star formation because working this way you kind of draw a big star.

Tighten each lug down till it almost puts pressure on the hoop. With the palm of your hand, press into the middle of the head so that the head dips an inch or so. Don't push so lightly that head doesn't wrinkle, but not so hard you put your hand through either. This will seat/settle the head on the bearing edge.

Now tighten each lug down until it starts to put pressure on the head. Still working your way around the drum in a star/opposites formation. Now there should be no wrinkles in the head. Give each lug another 1/2 turn, or just a little bit more so that each lug sits parallel to the edge of the drum, like this...

Tuning - Front head.
Repeat the above for the front head, then give each lug an extra 1/2 turn. This will tune the head a little higher than the batter head. If you prefer the heads tuned the same, don't do the extra 1/2 turn.

Hole in the head? A small hole is very useful for drums that are to be miked - for recording or gigging. Some heads are sold with a pre-cut hole. Ask your music shop to help you cut a hole if you are unsure how to do it (That way, if they wreck it, they have to pay for it or give you another one!). Anything from a 4" diameter hole, up to... well... no front head at all is ok. It's a matter of personal choice, I go for about a 6" to 8" hole. Just find something round the diameter of the size hole you want (Big coffee cup, splash cymbal, bowl, etc), place it on the head (Off centre looks better, at least 3" from the edge, for smaller holes), and cut around it with a really sharp knife. I prefer the smaller holes myself, as they allow the tone of a front head to add to the sound (like toms with 2 heads - fuller tone) but still allow easy miking. The hole also allows you to get at your muffling device (if internal) to adjust it if needed.

Be careful seating a head with a hole in it. Too much pressure may rip the head. Another way to seat a head is to hold the rim and turn it back and forth a few times, like driving the old Seasame St bus. This doesn't work as well as preassure on the heads centre, but it's better than nothing.

Muffling.
Muffling the kick drum gives the drum a punchier less ringy sound. The amount of muffling may also change the drums sound. People use many different things to muffle the ring of a kick drum. Pillows, towels, foam, blankets, newspaper, packing foam snowflakes, felt strips, feathers, rugs, and even external mufflers (blearchk! I hate those things.). It is a good idea to muffle both heads, and easiest to muffle both using the same item.

The idea of the muffling is to lightly touch the head in just enough places to remove the funny ringing sound produced when the head is hit (Sympathetic/harmonic tones.), not to smother the sound so bad the drum sounds like a big cardboard box.

If you lay the drum on one end and hit the head lightly with a stick, you will notice that just by laying some light cloth over 1/4 of the kick drum head that all ringing after the initial punch is gone. This is the effect you are after with muffling. Just enough light pressure on the head so that no overbearing ringing occurs after the head is hit, whichever method you use to achieve this is personal choice.

Minimalism is probably the best approach (In my opinion), so as not to choke the drum sound completely - from as little touching the heads as possible, to almost no muffling at all on kick drums. I use a rolled up towel. Roll the towel to make a snake. Place it inside the drum. Tape one end to the batter head, about 1/3 to 1/4 of the way up from the bottom, run the towel along the bottom of the drum, and tape the other end to the front head. Simple, light, and effective. Beer mats from pubs/bars are ogten just the right length, and even lighter than a normal towel. I pinched this idea from Herb, the old drummer from Primus.

Felt strips are also light. Before you put the heads on, simply put the strip across from top to bottom, or side to side of one end - only needs to go from 2 O'clock to 5 O'clock position. Hold it tight while tuning so that when your drum is in tune, it touches the head. This can be done by taping the felt strip to the outside of the shell to hold it place while you tune. Done. The end result is a dampening method that works really well, and takes up the least room in the drum.

Taping a small piece of cloth (One that holds static) is also easy and light. Static will help it stay resting against the head, and the duct tape stops it from flying away. Shouldn't need to be too big, but size will depend on muffling taste.

Pillows, blankets, rugs, cotton wool, and feathers are used in the same way - to put some light pressure on the head. Try and keep the muffling fluffy, as opposed to tightly wadded up. Also keep the contact against the head gentle and minimal, not hard up against the head. This will keep the dampening to a respectable level, and not choke the drum. Be careful that the muffling doesn't take up too much space. The room in the drum is for air to travel from head to head. The more you shove in that space, the more you interferre with the natural flow of the air and sound waves.

Double Kick Setups.
Most drummers have gone for the same sound for each kick drum. Drums the same size, same model, same depth, same make, same pedals, same beaters, etc, etc, etc. Same! On occasion the more daring drummers (like Cobham, Belleson, etc) have gone for different sounds on each kick drum. This is done a number of ways - different tunings, different depth drums, different diameter drums, different heads, different beaters, or a combination of these. It's really one of personal choice. Heads and beaters provide a subtle change, depth less subtle, diameter and tuning less subtle again - in fact very noticeable. With attention to tuning some of these differences can be quite melodic.

Protect the head from the beater.
Especially with wood beaters, having something on the head at the point of impact increases the life of the head dramatically. What causes the most wear and tear on a kick head is the impact of the beater, and the heat generated from the friction between the head and the beater.

For the past year I have been using a 3" x 6" rectangle cut from an old used head, duct taped to hang infront of the point of impact. The bonus of this method, is that I see the wear and tear on the rectangle of old head, and not on the kick head itself. I picked up this jem from Chad of the Chile Peppers. There are some products in music shops that are designed to protect the head that last longer. Some are teflon, some are plastic circles inside a cloth sticker - these also add a little click to the kicks overall sound that some mixers and studio engineers like (and some hate). There are models for single and double (2 in one) pedals.