1)How to make sure that my BTCQT is running against my custom datadir(what is datadir?)
Start bitcoin-qt with this argument:
-datadir="D:\Bitcoin"
Either run it from the command prompt or create a shortcut for it and add the argument to the shortcut's target.
2)Isn't the latest Armory 0.96?
There's been 4 testing builds out for 0.96.1 so far. Check the release page:
https://github.com/goatpig/BitcoinArmory/releases3)What does boostrap the DB mean?
Initializing from scratch, i.e. no existing state/empty folder.