General advice on sprite painting?

[Panpiper]

I thought I was doing pretty well, having come up with a half dozen unit sprites that looked pretty decent to me. I even uploaded them as the most recent additions to the mod I'm working on. Then I booted up the game to look at them (yepper, I should have done that before uploading).

Ouch!

A lot of what I assumed would be transparent turned out to be black. When I tried to use my fill tool to fix the problem, I wound up turning a lot of what should have been really dark, transparent. (I've since learned to adjust the 'threshold' of the fill tool.) Obviously I am missing a crucial insight as to how to start a new sprite. Should I be starting on a white background and simply 'fill' the white when I am done with pure black (the transparent variety)?

Are there some really obvious tricks that I should be aware of? (Seeing as how the obvious seems to escape me.)