How about he wears the damn suit under his clothes like he has since the beginning? Or maybe keeps it stored someplace secure and out of reach in a gym bag or something? (which DOES have precedent in the comics)
"But what about the boots?"
Maybe he wears a dress shoe size bigger or so to compensate. It's not as if he's wearing combat boots. Yeah his feet might look a little big... but then again who says Superman can't have smallish feet? The diesel physique makes his hands and feet look small anyway. Or maybe having the appearance of larger feet would help to emphasize the lanky and awkward Clark Kent disguise. How about... who gives a crap? (#IMAGINATION!)
"But what if his work clothes tear revealing his suit or he wants to wear short sleeves?"
Superman can walk on the sun, spends his free time in the Arctic, died, came back to life, and has fought every kind of weirdo/super-powered-alien-a-hole in the universe. I'm pretty sure the man can handle issues in both body temperature and clothing malfunction.
"Where does he put his cape?"
Folds it up? Stores it someplace secure? Do people really need an answer for everything? Yeah Superman can fly and stop bullets but can't handle finding a place for a cape...
Bottom line... to me, a magical Kryptonian nano suit requires more suspension of belief then any explanation one can conjure to account for how Superman manages life wearing his suit under his suit. It's a superfluous dues ex machina idea that just further removes Superman from being more relatable. It's real simple, just don't depict Superman fumbling around putting his cape on or taking his pants off or whatever. You wouldn't depict Superman taking a dump either. On the other hand...
now, see, to me, i find it more believable for a nano-tech suit to exist than him wearing it under his clothes. krypton was light years ahead in technology, so it's not a stretch for me to believe it could exist (especially if tony stark can make it exist, and he's just a human).
i always think of this snl skit when i think of the whole 'suspension of belief' with regard to the whole clark/superman dynamic:
http://www.trilulilu.ro/video-divertisment/the-rock-is-superman
amusing, yes, but it also brings up valid points.