I submitted a paper but I realized we accidentally commented out a couple paragraphs of the methodology. These are relatively important paragraphs, without which, I don't think the paper's results make sense (they're too good for the methodology without the added paragraphs). Do I withdraw the paper or do I add these in rebuttal?
Write to the editor, if possible, stating the problem and asking for advice. Waiting to update in rebuttal may be too late if you get a hard reject. They may have a way to let you update the paper now.
Failing that, withdraw and fix it for resubmission.
But if the editor can be reached and is helpful it would be the quickest way.
Waiting for the rebuttal could take quite a long time and if done well, the referees will notice issues if your omission is critical, leading to a possible reject.