If you're using the same pickup when switching between amp channels, then it's your amp's fault for the volume difference. Probably a preamp tube, if it's a tube amp.
If you're switching pickups and the volume is different, you need to adjust the height or maybe one of them is demagnetized/faulty.
You didn't say which pups you bought, maybe the pickups themselves are muddy...or you need to adjust your EQ settings. Muddiness is usually around 250-400hz
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