Rockinstrat..... Are you talking about the fine tuning pegs? All they are are additional tunning instruments. since most Floyd Rose briges accompany a locking nut, once you lock the nut down you can't use the pegs on the head to tune anymore or you'll just break strings. You have to string the gtr stretch the strings and tune it first, then lock the nut down. After locking the nut the gtr will be slightly out of tune again so you use the fine tuning pegs to tune it again it's usually less than a 1/2 step out. Actually the locking nut provides much less variation in the strings as far as going out of tune. What trendkillah is talking about are the intonation adjustment bolts. These do not stick out. they are there to fix any problems with intonations. They can be a bitch if they are out. It's best to have a professional fix any intonation problems. Intonations have to do with the physical length of the string between the nut ant the bridge. If it's too long or too short it won't tune to the other strings propperly. You should never mess with these if you don't know what you're doing.
Zeppo... sorry never played on anything with a tune-a-matic bridge can't offer an opinion at all.