Guitar company web sites are fine, but obviously they're going to be biased, so you'll need to find out what others think of the guitar you're considering. Fortunately, the web is filled with sites that archive user-reviews of guitars. Check the Guitar Review Archive for critiques of both acoustic and electric guitars. When studying these reviews, take special notice of the prices people paid for the instrument, and carefully consider all criticism. Be wary of people who give their guitar a "perfect 10" score - many of these reviewers aren't knowledgeable enough to offer constructive criticism.
Next, try using the Yellow Pages to look up other music stores in your area. You should consider visiting each of these stores to try out the guitars they offer. For now, call each of them, and see if they offer any of the same guitars you're considering. If so, ask to be quoted a price. Occasionally, you'll run across a store employee who is hesitant to quote you prices over the telephone. Mention you're about to buy a guitar elsewhere, and they should change their mind. Again, make note of any differences in price.
Armed with all this new knowledge about the guitars you're considering, it's time to take the second trip to the music store. I'd generally wait until the next day to do this - a clear head often gives better perspective, and besides, you don't want to seem too eager.