You mean different subdirectories of your working copy somehow got on different branches? You probably ran updates with the -r flag, but from places other than the top level of the working copy.
No big deal. If you want to return to the trunk, just run this
cvs update -r HEAD
cvs update -A
from the top directory. Or, if you want to put the whole working copy on one of the branches, do this:
cvs update -r Branch_Name
There's nothing necessarily wrong with having one or two subdirectories of your working copy on a different branch than the rest of it, if you need to do some temporary work on that branch just in those locations. However, it's usually a good idea to switch them back when you're done – life is much less confusing when your whole working copy is on the same line of development.