You are running version 14.2, the most stable release so far. That is good.
FBReader and Adobe viewer keep separate bookmarks and last-page-read settings.
Generally you want to use one or the other, whichever you feel more comfortable with.
If you like the philosophy behind FBReader (user settings rule!) you may want to try out the latest version of the SFF/GrayNM FBreader180:
If you prefer Adobe's reader but want some degree of typographic controls, you may want to look at the hacked version here:
The standard behavior is that if you are navigating your book folder structure, the book will open up in the default reader you define in extensions.cfg (see here: http://www.mobileread.com/forums/showthread.php?t=67149
(factory default is adobeviewer, btw). If you have already opened the book, it will open up with the app you first opened it.
Holding the center button gives you the context-sensitive menu, as you've noticed, and you can open it up with any reader. (Currently 4 possible options, with a fifth rumored on the way.)
When you choose a book from the LAST-READ list, it will open with the app you last read it with. Long-press does not work.
Adobe page numbers are calculated very different from FBReader and bear no resemblance to the number of screens it takes to render the full book on the PB360 which is what FBReader uses as page numbers, which is why the page numbers change when you resize in FBReader but not in adobe.
Some folks like one way others like it another; just figure out which you like and go from there.