i haven't had much luck using the pod with distortion pedals, though this isn't to say that you can't do it that way. i prefer the sans amp for this kind of direct thing. i record all my guitars direct, so the situation isn't the same as micing an amp, but what i've started to do now is record clean guitar tracks while monitoring with a pod or sans amp. i then run the guitar track thru
the revalver amp emulation software. this is similar to pod, but you can change your amp model after you have recorded. i only record this way cause i have too...i miss all the feedback.
is there a lot of noise with your guitar turned up, etc while you're not playing anything? if yes, you might want to reevaluate the setting on the pedal and the amp....to be more precise, is the noise very loud when you aren't playing?
what kind of amp is this?
i think the last thing to do is to plan to use software to clean up a recording. use software, yes...but first get the sound you want , record it and then process it however....
of course using a noise gate, or some kind of gating effect, is , i think, almost a must with digitally recording heavily distorted guitars.