To make FFTW work on a new platform, make sure the sysvars file includes the path of the FFTW library (for example, see sysvars.sgio200). Secondly, you must make sure that if the platform also supports a native FFT package that M4FFTFLAG is defined (again, see sgio200), and that adjustfft.fp uses that value.
I think that is all that should be needed. When you run the configure script, of course, you must say yes to fftw.