To solve this problem, most players set up a compressor/limiter after the filter. Putting one before the filter changes the filter response, which is not desirable IMO. If you put a compressor after the filter effect, you should set it up as a limiter. For your pedal, set the attack all the way left, the release in the middle, and the ratio to 20:1. Set the input so that the meter lights up only on the hardest notes with the filter on. Now set up gain to taste.
Basses: Fender Am Std P5 (x2)
Amp: ShuttleMax 9.2, Fearless F115, F112