I don't partake in big stupid tv's or anything like that, but the best way to wire anything is from the ceiling if possible.
Or basement.
If you want a real suggestion, get wireless rear speakers. Wiring rear speakers in general is a BITCH. If you don't do wireless speakers, plan to do drywall work and repainting. Personally, I try to stay away from patching drywall because most of the time it looks worse than a full sheet.
Most home theater systems are setup 100% wrong. First and foremost, the middle of your TV screen should be at eye level from where you watch TV. Have fun watching your TV mounted on top of your fireplace. You will have a sore neck in 30 minutes flat.
As for speakers, your front 3 channels of your surround sound system should be directed at your ears and at ear level. Speaker distance should be equal. Meaning, don't put your right speaker 10' from you and your left 20'. It will create an unbalanced sound. Where you mount your rear speakers is less important as they just offer background music.
If you plan on mounting your TV on the wall and using a low entertainment center, you can tunnel your speaker wires through your main tunnel and then put a shelf underneath the TV or one to the right and left of the TV. Put pictures and shit on the shelf but also use it to hold your speakers. This is a great way to mask your speakers and create cleaning wiring. Otherwise, I suggest getting front speakers that are on floor mounts. Again, fishing lines behind drywall will result in lots of patch work, painting, and cursing. I avoid it whenever possible.
http://www.crutchfield.com/App/Tab/Learn.aspx - They have great writeups on how things SHOULD be done.