I paint from the bottom up; so I do the below-waterline hull even if it's a darker paint than the above-waterline paint. Two reasons are that I find it much easier to mask (see my article on airbrushing ships here) in that order, and also, because the above-waterline is painted later, any paint ridge is harder to see since you are looking down on it. For things like dazzle schemes, 99% of the time I will go lightest to darkest.
The other advantage to this is that *if* you have a secure mount to your stand, it gives you a good work hand-hold you can use without having to handle the hull and get fingerprints on. I usually fill the bottom quarter inch of hull with resin, though, to make sure I've got a good grip that won't split the hull seam, etc.