The best way to seam the sides of a garment is mattress stitch. Shoulders are often done with a 3 needle bind off for stability. Here's some help videos and tutorials.
Mattress Stitch - scroll down to finishing in the first link
http://www.knittinghelp.com/videos/knitting-tips
http://www.knitpicks.com/tutorials/M...itch__D42.html
http://knitty.com/ISSUEspring04/mattress.html
I weave in ends like this -
http://www.knitty.com/ISSUEfall04/FEATfall04TT.html
There are 3 needle bind offs on those first two links. If you've already bound off the shoulders here are some other techniques -
http://knitty.com/ISSUEspring06/FEATspr06TT.html