Is it difficult to do a post-break-in wheel tune-up? I've heard that when you get new wheels you should put a couple hundred miles on them to let everything get set in and get an initial stretch, then do a tune up.

Can I just go by feel and tighten the spokes that seem a litte lose?  I don't think the wheels are untrue, they're heavy duty wheels.  Are there any tricks to this initial tune up?
As has been mentioned in the comments, you should take it to a shop. You're likely to do more harm than good if you're not already experienced in at least truing and preferably building wheels. 

It also might not even take a couple hundred miles. I'd probably check on it once a week or even every couple days. Feel the spokes. Once it gets to a point where there are notable differences in tension, go ahead and take it in.