So I just picked up the boss rc300 loop station and it's awesome. The one thing I cannot figure out is say I record a loop with a clean setting, but then want to play with a dirty setting, how do I change the amp channel without affecting the loop that's already been recorded.

Thanks for your help
You cant. If you put the looper in front of the amp, changing the channel will affect all loops. If you put it in the fx loop, changing the channel wont affect them at all. You could route the loop trough the sub output and then trough a distortion pedal to get dirt. And there also may be a 4 cable method for loop stations, but i dont know about it.
Joža je kul. On ma sirove z dodatki pa hambije.
Pretty much ^^^

Put it in the effects loop. If you don't have an effects loop then put it at the end of your chain, but any AMP settings will affect it.
Gibson LP Standard -> Helix -> Art Sla-1 -> Mesa Boogie Thiele 1x12 (C90)