So it's been over a year and you're still wondering how to buy a bike that fits well?
If you're not confident with the staff at your LBS then you could learn a bit about bike fitting from sites like these:
http://bikedynamics.co.uk/index.html
http://www.peterwhitecycles.com/fitting.htm
http://www.sheldonbrown.com/frame-sizing.html
Then go to the shop with a basic understanding of what you're trying to accomplish and start from a 'neutral' position such as:
- Seat mounted mid rail and adjusted such that your heel just brushes or just misses brushing the pedal at full extension without 'reaching'
- Hands up on the brake hoods with elbows relaxed and comfortably bent, back straight.
You shouldn't feel either cramped up tight nor have to go to great lengths to stretch forward to get your hands on the hoods nor should you have to hold your arms straight and unbent to reach far enough forward. IOW, you should be able to simply relax into position that places your hands at or very near the brake hoods while sitting centered on the saddle with your back relatively straight.
If you can achieve a position like that or like those shown on the linked websites with a fair amount of seat post showing and with a nominal mid length stem then you're probably close and have room to fine tune your position over time. A 'fair amount' of seat post is pretty vague but I'd generally want to see at least 10 to 15 cm of seatpost above the clamp but with plenty still in the frame so you have room to both go up and down as necessary. Similarly I'd be looking for that fit with a stem in the 9 to 12 cm range for most adult men, perhaps a bit shorter for folks that aren't that tall and for many (but not all as in the example posted above) women. If it takes a 6cm or 14cm stem to get a comfortable 'neutral' position then you're probably on the wrong frame.
If the basic position seems reasonable then you take the bike out for a test ride or two, hopefully more than a parking lot ride but definitely get the bike in motion and have the shop move things around and ride again if it doesn't feel right. You don't need to go out for several hours or take the bike home to get a feel for it but you do want to actually ride it.
The basic advice is usually to choose an LBS that knows how to fit and allows you to test ride. That's still good advice but if you're not certain how strong their fitting skills are then you basically have the choice of finding another shop or learning about bike fit yourself. The latter can be useful regardless of where you buy the bike especially since appropriate fit and positioning tends to change over time as riders become more experienced and their fitness and flexibility changes.
Good luck,
-Dave