How will I know when they need to be transplanted a second time.

I would advise against transplanting them a second time until you are ready
to plant them outside in the ground. Depending on the plant, give it a
suitable sized container when you re-pot them (in other words, large enough
so that it won't out-grow it). If it does seem like it is getting root
bound, don't fret too much. Like you've already pointed out, store bought
plants are a virtual ball of roots. When you re-pot them, give them a weak
drink of transplant fertilizer, then again when you transplant them outside.
Of course, having said that, every gardener has ther own special formula of
success -- this is just what works for me. Also, be sure to give them plenty
of light so they don't get spindly. I use adjustable flourescent grow lights
that hang just a few inches above the seedlings.

--
Shadow
Made In Canada, eh.