What I do--and everybody's method varies--is write down these swell ideas in a separate document. Before I tackle the second draft, which is always a few months later, I rewrite or revise my master plan, incorporating some of those ideas. Their presence means some things change so much I have to write new material and delete whole scenes, and other aspects can be lifted intact from the first draft.
Note that I do not change my first draft but create a new document for the second draft, copying and pasting what I can. That way if I decide no, the first way was better after all, I still have it fully intact.
Maryn, hoping this helps a little