First off, based on your questions, I would recommend learning what the FFT actually is and how it works on a fundamental level if you want to try to control it. Read Appendix C of my master's thesis which is on my website under software, or the appendix of the computer music tutorial by curtis roads.

If you want 64 bins spaced from 0-400, you would need to have a 128 sample window for the FFT, and the sampling rate would have to be 800 Hz. Remeber, window length needs to always be a power of 2, and your bin spacing is Sampling Rate / Number of Samples per Window. You could also use a higher sampling rate, a longer window, and just use the output of the lower bins where the cutoff is closest to 400Hz.

As far as interrupts, the Interval_Timer library is a pretty good route to write your own interrupt/ADC routine, and then you need to store your samples in blocks of size N for processing by the FFT. If you're clever you can double buffer and overlap your windows so that while one block is being processed, you're still collecting samples for the next block.