How can I detect potholes using an accelerometer mounted in a vehicle?
You are not really interested in the frequency information in your signal so much as detectable features - as such I would suggest that there isn't that much utility in an FFT here.

What you really want to do is correlate the continuous 'car signal' recorded in the car with a different signal which is the 'signature' of the pothole bump. You will need to acquire this signature by recording it in a car going over a pothole (perhaps recording many and using them to produce a generic signal which is a good representation of a pothole). Once you have it you can cross correlate it with your car signal. You may want to do this in the frequency domain in which case you should cross correlate the FFT of your signature with a sliding FFT of the car signal.

You may want to process the car signal before you use it to remove, for example, high frequency noise (with a lowpass filter). You can do this pretty effectively by eye - play around with various filters on car signals to see which removes the most extraneous information while leaving the important pothole information intact.