One of the dangers of using a friendly pill to block the shots from an enemy pill is that when you are done, there are two dead pills sitting there, ripe for the poaching. The best way to avoid losing both pills is to rebuild your pillbox fast enough so that nobody but you and your allies can get near the booty. Here's how:
Before you start taking the enemy pill using your pill as a block square, check to make sure that you have selected the pillbox building tool. Watch the friendly pill carefully: if you time your builder wrong, it will die a horrible death.
Your pillbox will die before the enemy pill does. The INSTANT you see your pill die, send your builder out to fix it. Finish killing the enemy pill as your builder is on his merry way, then turn and accelerate away to avoid the last stray shots. Ideally you should turn so that the enemy pill will shoot away from the pillbox your builder is about to fix. You have about one second (lag free) between the time your pill dies and the time the first bullets from the enemy pill hit you to send your builder, depending on how close your pill is to you. If you send him too early, the enemy pill may kill him as he is rebuilding; if you send him too late, the shots from the enemy pill hitting your tank will kill him as he leaves.
Also keep in mind the state of the terrain between you and your pill. If your pill is surrounded by swamp, you can safely send your builder out several seconds before your pill dies (depending on lag).
The problems with this method are few. The worst problem is predictability. If you repeatedly rebuild your pill in the exact same way, it becomes pretty easy for a good opponent to anticipate the position of your builder and kill him. To avoid predictability you can try these tricks: rebuild the pill before you see it die (this is more difficult but possible); don't rebuild the pill immediately, and use another pill to guard your spoils (Santa likes to do this); use 2 pills, or a pill and several walls as block squares so that you will have full armor when the enemy pill is dead, and will be able to protect the dead pills from a poacher. Another safety measure which takes some skill to execute: start taking the pill but stop before either pill is dead. Retreat and fix your pill then go in and finish off the target pill. This method will leave your pill angry and you shooting at the dead pill, ready for enemy builders.
LAG: if you are rebuilding your pill in heavy lag, you should not attempt to rebuild it until you see that it is dead, otherwise you will almost certainly lose your builder. You may lose your builder anyway, because lag sucks.
(sluggo was the first player I saw use this rebuild method, so thanks go out to him)