Compressors iron out those notes that occassionally boom, so you never really notice them working. I just have a little compression on my amp always on. It does affect your tone, but it also keeps things like my pedals in check, so, for example, my bass micro synth gets louder as it gets lower (as I like extra bass on my pedals so it gets louder), and it just quietens the pedal down a bit and levels it out. If I had the money I'd put each pedal in it's own bypass loop with a compressor/limiter for each pedal to tune it for each pedal.
But I'm fresh outa cash