Separates are higher end usually and cost more money for better performance. Separates are probably worth considering if you're setting your system up in a large room, or if you are using low impedance speakers. Even then, high end integrated amps, like THX Ultra certified ones, should manage reasonably well here.
I've got a few links that I've pillaged over the past year or so:
http://www.homecinemachoice.com/articles/hccarticles/interviews/FloydToole/FloydToole.php
- This one's an interview with acoustic expert Floyd Toole.
http://www.hometheaterhifi.com/volume_9_2/feature-article-curves-6-2002.html
http://www.hometheaterhifi.com/volume_7_2/feature-article-dialog-normalization-6-2000.html
- This one's some background on cinema sound and Dolby Digital dialogue normalisation.
www.rane.com
- Lots of useful technical info under Rane Notes, etc., particularly:
http://www.rane.com/note128.html - about power amp clipping. There was a very good THX/Rane article on RTA analysers but I can't find it now.
For positioning your front, full-range speakers, try to allow 1 metre depth from the back wall and 1.5 metres from the side walls. Symmetry in set up and acoustics is best for good two channel stereo performance.
I myself have found sub/bookshelf combinations problematic, but there are advantages to having such a set up. The bass will sound similar across all three front speakers. You can have smaller front speakers. The difficulty is in getting even frequency response and this will usually require equalisation. The Miller & Kreisel website has more about this -
http://www.mksound.com/.