Signal compare - cross corelation in frequency domain matlab
Yes, cross-correlation will provide some information on the similarity of the two waveforms. See the function reference for xcorr. Look into proper normalization so that the result is between something like 0 and 1 or -1 and 1. As a matter of fact, this is pretty well discussed in another stackexchange question.

As for frequency domain cross-correlation, I don't think that's what you want to do. Doing time-domain cross-correlation results in multiplication in the frequency domain, so you're looking to maximize the total energy in F(x)*F(y), where F(x) is the FFT of x.