You should tell us if your using windows or linux and maybe explain a bit more about what your trying to do exactly(why you are adding flags etc).
I know on linux you can define some compile time values when running make as described
here for run in place and
here which is a list of all cmake flags.
I guess you can pass flags using "cmake . -flag1 -flag2=x ... etc" but, as I said, I'm just guessing based on the documentation and not experience.