If the bike shop is a good one, its worth using it. You may need them for servicing later. Online buying is for when you know exactly what you want and can assemble and tune bikes well.

Make sure you get the right syle of bike. A competition road bike is good for racing or fast day rides, and Specialized are as good as anyones, but not so useful for commuting, slower paced long rides ,less athletic riding, hills, light touring, commuting. For these kinds of riding a sport touring bike is better.
Jamis make a nice example
http://www.jamisbikes.com/bikes/aurora02.html

and so do a number of other makes, but Specialized dont do it.

For advice on fitting a bike, check out

http://www.peterwhitecycles.com/fitting.htm