Usually I don't add until prc is read. During reading I just make bookmarks in palm, depending on those what to do next - if there's just few typos, I may create txt after finishing whole book, if lot of typos, I enter them in txt (and delete bookmarks) once in a while, if there's some irritating formatting, I also correct the typos I found so far and make new prc... All without touching Calibre.
Finally, when I'm reasonably happy, I delete copies I made of html (just in case I change something major and don't remember what was there before) and add all 3 files (ace, prc, txt) to Calibre, then merge them into original entry.
I use mostly Mobipocket Creator - it's much faster (takes 1-2 seconds to convert, easy to check if I managed to push text to the right margin for example), makes toc in the beginning of the book and is less complicated (and probably allows less control, but that's ok for now).
If I'd used Long Text field: every time I'd have to enter Calibre, find the book, (scroll), find Notes field to add things.
I don't need the notes about formatting to be searchable in Calibre (yet), if some reason crops up, I'll probably think up a tag (chektxt, noitalc). So far quality rating is enough for me.