I haven't studied the Schönhage–Strassen algorithm closely so take this with a grain of salt. But I think I can give you at least a vague, simplified sense of how the FFT is relevant.

Multiplying polynomials is the same as convolving their coefficients, which is the same as multiplying the Fourier transforms of their coefficients (this is the convolution theorem), which can be done efficiently with the FFT. Now a base-10 number like 971 can be represented as the polynomial 9x^2 + 7x + 1 evaluated at x = 10. So multiplying base-10 numbers (or base-whatever for that matter) can sort of be seen as a special case of multiplying polynomials (plus a step afterward for carrying the digits), which can be done with the FFT.