is it better to run stompboxes trough the input or through the effects loop,i have a awsome marshall jcm 900 and don't want to get away from it's thunder by not having it sound like a line6 fake sound
It depends on the type of effect you are using. Boosts, overdrive, distortion and wah pedals should go into the front input of your amp. Delays, chours, phasers, etc should go into the loop.