I have my story planned ahead and I also experience this "ideas popping into my head" thing, but I mostly tend to think long and hard about which scene to put where. The decision process can sometimes slow me down quite a bit, but just not thinking about it, is not really an option
I think about it constantly. About things like pacing, order of the scenes, dialogue and how to implement certain plot points naturally and of course how to do the layout (and throwing it overboard completely once I actually need to draw it, lol).
My comic also has some complicated political themes (coughterrorism*cough*), so I agonize a lot over how I portray these things. Do these characters come off as too sympathetic? Are there biases I put into my work, that could be harmful considering the content of my comic? Am I misusing the backdrop of my world badly or is it to heavy handed (I'd say this is a definite yes, haha)? Things like that. This sort of thinking is rarely productive, as I won't come to a conclusion myself. I need the help from readers to actually see if my story comes across the way I hope to. But I can't help myself, I think about this a lot, even though I should probably just use my time more constructively and actually work on the story itself ^^