To quickly answer one portion, ensure iTunes thinks your audio books are actually audio books. Then it should preserve the position information, and even sync it back and forth, allowing playback to resume on the PC if you want. Here is the quick way to change this using iTunes 8: link

As for the rest, I'll have to let someone else step in. My iTunes usage has been limited to OS X only, and set to let it manage my music. I can say that on OS X, holding Option (alt) when launching iTunes allows me to point it to any drive or location to make the library folder. This may be similar on Windows, likely by holding down Control or something when launching it.