As for the route, I'd say just try it out and see which you prefer. I tend to prefer side roads as I can deal with folks backing out without looking pretty easily. On the down side dealing with stop signs/intersections every 5 feet gets old.

For wardrobe, if you need to look your best then I would probably ride in workout clothes and put my work clothes in a bag (rolling helps prevent wrinkling). If that doesn't cut it, I would consider a garmet pannier such as this one: http://www.nashbar.com/profile.cfm?sku=21437

At the very least if you are riding in pants, you will need something to keep the bottoms out of the chainrings/chain such as a chain guard or one of those velcro reflective bands that every shop usually has on the counter.

For a rack, if you are considering any sort of pannier, I would highly recommend a Tubus. One with two sets of top rails, such as the Cosmo and Logo, allows for panniers and a trunk bag to be mounted at the same time easily. Should also help keep the panniers out of the spokes. Check out:

http://thetouringstore.com/
and
http://biketrailershop.com/catalog/index.php

If you aren't going to be using a pannier, than you may be satisfied with one that just connects to the seat-post.