I think it depends on what pedals you are using and the order of effects comes into play as well. Distorting before or after adding another effect makes a difference on the sound.

Consider if you had no distortion pedal, the amp's gain would be the last thing added, and it would be perfectly valid to run a Flanger thru the distortion channel, right?

Sounds like you have some multiple effects on your amp. If there are none on that channel you needed, I would run thru the clean channel. Otherwise, I do know hooking "dual distortion" can create some awesome feedback. :) You could turn the gain on one or the other to 0 I guess.