I am not sure what you mean by synchronizing the frequencies.
To do the modulation you should have the sampling rates the same and the array sizes the same. Currently you appear to be limited by the size of you code array, 512 or 511 elements.
The attached file has both the sine and square waves generated with the same sample rate and the same number of samples. The product looks like BPSK where the modulation rate is much faster than the carrier frequency. The spectrum is rather random.
Why are you using size of 2 for the FFT? The Fourier transform of two points is completely meaningless. You need several cycles of the lowest frequency to get a decent spectrum.
Lynn
