I bought a bike from Bike's Direct intending it to be for my wife, and it was slightly large (which was my fault, but more on this). It's a fine bike, great parts, etc. It was easy to put together. I also bought a bike stand, and I have a bunch of 'regular' tools, and a multi-tool, although I ended up not having a 15mm wrench for the pedals (my set skipped from 14mm to 17mm or some reason), so I bought one of those too.
Anyways, before returning it, I decided to figure out the sizing thing more in depth, reading here, and elsewhere and at the moment the conclusion I have is "No one knows what fits you but you...after riding for a long time." I could be wrong.
So that bike fits me fine, and I was going to get one. I previously was riding a 2009 Kona Smoke, which is basically a mountain bike with road tires. The Kona worked fine for commuting, but I was certainly looking to upgrade soon for longer rides (perhaps I subconsciously ordered too big, heh). I also have a much more intense biking buddy to ask advice of and get tuneup help for the low, low price of a sixpack of Sierra Nevada, and I drink half of it. Deal.
Now, right, why did I end up ordering a slightly larger bike than I should have? My wife and I visited a bunch of LBSs looking at bikes, and I bought my Kona from an LBS. Even my biking buddy suggested the LBS. However, no one seemed particularly consistent on fitting style. Maybe my budget of < $1000 hurt, but they all seemed nice and helpful, it just didn't end up helping. No one really explained the differences in stem length or anything, it was almost all "That looks like it fits you!" One guy seemed very nice, and had my wife on a 54 Trek, saying he thought even a 56 might work. My wife is 5'' 4.5", but I figured he must know more than me, so I ordered a this 54cm bike, going against the BD fitting suggestions, figuring after checking everything the LBS guy must know a lot about fitting, and his vast experience was all cumulative into the "That looks like a good fit!" Now, not all the LBS guys gave the same fit, and being new to roadbiking, neither my wife, nor myself really know what's really "comfortable". Her old bike, an Electra Amsterdam, is really very 'comfortable' until you want to go fast or up a hill.
After that, I saw a Fuji Roubaix 1.0 on sale at a local Performance Bike shop for what I seemed like a good price, and we ended up buying one of those for her instead of going the BD route.
So I would a) contact Bike's Direct and ask them about sizing (they do run their own stores in Texas and some other states, btw), which I should have done (Yes, I'm stupid sometimes) and b) ask the LBS if you aren't happy with the bike's fit how long you can exchange it for. If you don't want to wrench, just buying from an LBS might not be cheaper, one of my favorite bike shops sells only some old rehab'd bikes, and is mostly a parts/maintenance place, and seem to have lower prices than most others for LBS.
Your mileage may very, but I don't think either online or the LBS is necessarily better, depending on your level of wrenching/budget.
I've still bought plenty of stuff from multiple LBSs (actually I bought a used fuji for my son, too, and another online bike for my step-daughter, yes, having a family makes every activity ridiculously expensive to get into), but without a sale, for me the online pricing was a big winner. The "fit" expertise certainly hasn't been high enough to make me feel the LBS is worth the extra dollars.