I don't have much experience myself with finer points of installation, various means of hiding wiring in particular. Below is a quick link I found at one of my primary forums. Also, if Mike decides to talk shop on his off hours, he may provide some insight.
http://www.avsforum.com/t/1274911/diy-how-to-hide-wires-and-cables
Seems like the primary options is through walls / behind drywall, or behind your baseboards/moldings.
I have seen a number of center channels mounted above a TV. The most common recommendation when going that route seems to be to make an effort to angle it slightly down towards the listening position.
The subwoofer placement is a hot and common topic. Largely due to the wavelengths of the frequencies coming from the subs being large (meters/feet instead of cm/inches) - sub placement can be very room dependent. There is a famous 'sub crawl' approach where you end up evaluating as many locations as you could possibly stand to have the sub located, and see which provides you the best response. And it's a slippery slope from there, where the best approach is to have multiple subs!