even when I do specify -datadir it doesn't load the bootstrap file...
Check the debug.log IIRC there is no "Im using the file you gave me" message in the GUI. To your other question: what cr1776 said.
-snip-
From what I read it's faster to just download with the client than to download the bootstrap.dat separately, but surely it's faster to use bootstrap.dat if you already have it, right? Maybe I'll give it a try later and see how it goes.
Depends on the systems bottleneck, but it shouldnt be slower if you already have it.