My piano teacher always used to lightly circle every note in a piece that had a flat or a sharp. I found it very helpful. Make all the marks you like I think. That's what sheet music is for. If you watch professional musicians playing in an orchestra they are always marking their scores.
Fingering and marking by: Eddie
Marking flats/sharps on scores, I feel, shouldn't be done. You must be able to remember the lowered or raised notes on your own. Do it enough times WITH a very familiar piece and you'll be doing almost magically. Now, fingering...
What every you feel comfortable with is generally well accepted by most pianists (except for classical playing). When playing chords (not scales-- these should be played in the most efficient manner, and that is what most scale exercise books show), if it feels right to you, then by all means go there! You will find, however, that playing a triad, say, C maj, with (right hand) thumb, first finger, ring finger, will be the best way, especially when you're going for 4-note and 5-note chords.