I would advise at the beginning to limit the books added to the library. 100-1000 is nice to look at, but pita to change. After many-many months I am still deciding exactly what metadata and where and in which format I want it. I may hide the column, but I still want to have the information.
I keep all kinds of formats in Calibre - original pdf/whatever, aced files if I used mobi creator, final prc or mobi, txt where are notes about what I did (like, 'lit>epub, html>prc. Added such and such things, need to add...etc').
I can use only mobi when away from PC, so finding/choosing suitable format is no brainteaser; if my needs change, I'll convert before reading to different format.
About refixing - I find text file with notes to be handy. I note there what irritated me and if I fixed it; if I ever want to read it again, it's easy to decide what to do, if not...