First I pick a panel to test my product/pad combo (unless I already know what's called for), and for that panel I pick something easy to work, like the trunk lid or a section of the hood.
But for the actual job I too start with the roof. If it makes a lot of dust or some other mess it seems to work out the best that way (e.g., less chance of messing up previously finished areas). And I usually stand on work platforms when doing the roof (I'm 5' 10") and after I get that part of the vehicle finished I can move the platforms out of the way.