I have to say, my joins never look totally neat so I'm afraid I can't really advise you on that, but I can help you with the colour changes.
Because knitting in the round isn't technically round upon round upon round, it is more like knitting in a spiral, kind of like a spring, so if you can imagine that you can see how the end of one "round" would be higher than the beginning of that same "round". What you need to do is a technique called the jogless jog
. It will make your stripes look much neater and the colour switch will be all but un-noticeable.
Edited to add: I just found an article here: http://www.knitty.com/ISSUEfall03/FEATtheresa.html
that gives loads of info about circular knitting, and also a few tips at the very bottom of the article for making the join neater.