A major consideration is whether you're going to go with one system or two. I love both music and HT and space dictates one system, so my focus is on making a system that is as good as possible for both which, necessarily, involves some compromise. I'd make that decision first.
For HT, I'd set up a simple 5.1 setup (though agree with Sean that even 2-channel HT is a HUGE upgrade over straight TV). I'd set my decoder on Dolby Digital and forget about it for a good long time. There are more formats coming out every day. They undoubtedly have a lot to offer. You might decide you want to pursue them some day. But for the time being, brand new to this part of the hobby, I'd just do DD and forget about it. Every DVD is compatible, no confusion, lots of fun.
For your rears, use whatever you have laying around, at least to start. The front three really need to be a matched set, but the rears can be fine as just a pair of decent speakers set up in back. Again, if you find yourself loving it, you might decide to upgrade them, and there would be benefit to doing so, but the basic experience will be there without spending more to get matched rears.
If you go with a single system, you'll have to decide how you want to optimize for sound - there are many more things that might matter to you in a combined system than in a 2-channel, music-only system, unless you decide up front that you're going to optimize completely for 2-channel sound. There are many threads around detailing how you might achieve better sound for both through various options. Lots of gear to choose from, most of which has significant strengths and weaknesses.
I sympathize with your audioMart experiences - I can't find anybody at any store who offers any kind of real advice. I think anybody reading this forum knows LOTS more than most people who make a living at this about gear just by reading the magazines and forums, etc.
Hope this helps. -Kirk