Ride with what your the most comfortable with, just because clipless is the new black, doesnt mean they're for everyone, ya know? I'd rather drink milk from a goat dick then ride with spandex and clips..
I just realized that was kind of irrevelevant to what you asked, lol. I'm sure you'll get used to them, and you might even have to weigh out the pro's and con's of them, if the power you get is more satisfying then the comfort of the flats, then ya know what to do. I dont really know anything beyond my own personal expierence about it, though.