RE: Coffins
You may have as many as you like, but the rule ist that you need a layer of dirt fully covering the bottom of the coffin that is from the land where the vampire was created (Waterdeep environs).
Each one of you has a stone coffin in a room in the inn/tavern that cannot be accessed by mortals. The room can only be entered by creatures that are able to bypass near-solid walls. There are six cracks allowing passage into and out of the inn/tavern. Likewise, the stone coffins can only be entered in gaseous form, so it is a major challenge for mortals to challenge you while sleeping.
You don't need to worry about your 'home coffins' being destroyed as that is unlikely to happen.
RE: Running Water
The water needs to be awide and deep enough to be fully immersed in it. Since a vampire can't cross an ocean in one night, they need to have their coffin aboard a ship in order to be able to cross it. Also, see the Rogue's Gallery for the template information on creating vampires.
A river or stream can be crossed if the water is absolutely still. Not being able to jump over a gutter full of running rainwater is ridiculous, so you don't need to worry about that little nuissance.
RE: Staking
The vampire needs to succeed on a Fort save where the DC is equal to 5 + twice the amount of hit dice the vampire has.
Failure indicates that the vampire must instantly revert to mist form and retreat to its coffin or is immediately slain.
Success indicates that the vampire takes no ill effect from the attack.