You might be able to do a classic slip stitch technique, using a crochet hook. This is nice, if you are looking for a "stretchy," flat method of joining panels, but if you want firmer, "constructed" seams, you need to overlock (without a trimming knife), or tape seam, with suitable machines. Although I linked to an industrial machine site for sake of illustrations of seam construction, you can do very similar work with common 4 thread home serging machines, at much less cost, if you take your time, and adjust the machine feed and loopers for the uneven nature of hand knitted goods.

Have you blocked the pieces? If not, that may help considerably. For an invisible seam, I've found that it helps to work from the outside of the pieces so you can see what the seams will look like as you work. You'll want to stitch through the loops rather than the knots along the edges and try to keep the yarn tension consistent and not too tight.

If you have a good yarn shop nearby, they may very likely be able to lend you hands-on finishing tips -

Good luck!

Sorry it took so long to get back here... take a look about halfway down this page (v. helpful knitting videos) for Finishing Techniques > Mattress Stitch. Not having seen the edges of the pieces that you're working with, I wonder if this stitch will work?

http://www.knittinghelp.com/knitting/basic_techniques/misc.php