Congratulations on the new home and welcome. Some area that would be helpful so people can give recommendations would be:
1) Size of room
3) Goals (IE: room shaking bass or in-wall speakers for aesthetics, etc)
4) Listening habits and percentages (system will be used 50% of the time for TV 50% for music, used for background music, I like to shake cats out of trees from a block away, etc).
5) Previous experience with audio systems, what you liked/disliked.
Nick has some good points, I will add to that list.
First have a read through some of these posts as they will answer some if not most of your questions.
Also What kind of display are you thinking of using? (projector or flat screen).
Things to stay away from if possible, square room dimensions and a rectangular room that is a third longer than it is wide. As these two sizes (to put it simple) will do strange things to the sound.
Do not go with in wall or in ceiling speakers unless absolutely necessary as you sacrifice sound quality and cost as much as three times as much to get the same quality as floor standing or bookshelves.
Is the room you are using already finished, drywall up? I would have wired the room for 7.1 sound first. A buddy of mine was having his house built and on a off day when the construction team wasn't there me another guy ran all his speaker and sub wires in the wall so he would be able to mount nice neat wall plates and make his wife happy not to see any wires along the baseboards.