Until you can do a trackstand for a considerable amount of time (at the beginning, say, 30 seconds), you definitely do not want to be clipped in. You will try to plop your foot down because you feel the balance fading out, and you will struggle and topple over. Not fun. If you have ATACs, SPD's, eggbeater candies, or another flat-ish clipless pedal, you can definitely just learn how to trackstand while standing, unclipped, on the pedal surface.

Once you feel pretty comfortable with trackstanding, and feel as though you've mastered balancing yourself even if you wiggle around, take a hand off, whatever, and become proficient terminating trackstands voluntarily (as opposed to -- "uh oh, i feel like i'm going to fall down now" and stepping out), by all means clip yourself in.

Learning to trackstand is all about trial and error -- don't threaten yourself by clipping in and suddenly needing to clip out too quickly.