Sounds like you've been shopping at Magnolia, yes? There is much more diverse help online. There are a couple of other sites that may offer faster responses and there is also a VideoGon which focuses on Home Theater.
There are three main disciplines in audio reproduction: Two channel stereo, multi channel audio (five channels of unprocessed audio only, speaker selection and placement is as critical as stereo), home theater (multiple processed audio channels generally diffused by the presence of a video display and a dedicated center channel speaker of a different design).
Being new to this stuff it's important to slow down and learn as much as you can about your particular application. There are many low cost and used products available that can take your audio experience far beyond what's offered at the mass market store. You touched on one of the most important components in any audio system, your room. Before you spend any money you should locate a two channel system that's properly setup so you can experience soundstage, width and depth first hand. Locating an audio club near you would be an ear opening experience as well as a chance to meet some unique people. This first hand knowledge is very important even if your interest is in multi channel or H/T. While there are audio shops that have listening room's they're typically not realistically set up, your home is not a post production studio.
Typically, most people put the stereo in front of the H/T (setup wise). Many newer preamps have a feature sometimes called 'pass through' which allows the signal from the stereo preamp to feed your H/T preamp/processor/reciever. Unfortunately I have been unsuccessful at integrating a two channel system with a home theater and I've happily settled for a satisfying two channel system and a mediocre H/T
