Use clipless if you're skilled with them. I would not use non-clipless pedals on my bike for my commute, or even for the mile and a half to the grocery store, or to the store 3 blocks away. I hate how they feel, and I'm less stable on them. But, when they were new, and if I had been a cycle racer, I wouldn't have used them in a race because I'd false-start for sure.

If you don't like clipless pedals, just jump on in whatever you're wearing. Chances are if you're fine riding in your NBs, you're good; that much flex (NB soles are stiff) isn't going to hurt.

Also, for running, get some Vibram Bikilas or KSOs or Sprints, if legal. Bikilas are the purpose-built for that.