Basically what you want to do is run in-wall rated speaker wiring from each pair of speakers, in each area, in what is known as a home-run configuration to where you main entertainment equipment resides, including your main TV.

If everything comes in to that point then later you can decide upon receivers (such as multi-zone), speaker selector switch, etc.

In each room you may wish to install in-wall speaker level controls so that they can be controlled individually in each room.

As far as speakers, most decent quality ones are going to be fine but the variable is your ceiling... sometimes insulation needs to added over the speakers and sometimes reduced - sometimes extra screws need to be added to the sheet rock, etc. Also in two story homes you got to remember one room's ceiling is another room's floor!

Good luck.