I paint after assembly because I think its easier. Restoration freaks tend to paint before assembly because it is more authentic, but it requires more masking and attention to detail.
I agree with the others; unless you're doing a special POR15 engine paint, I wouldn't use it. Its great as a rock hard topcoat for rust, but you'll have to topcoat it and I don't think its best on hot engine parts. I have great luck with Eastwood rattle cans of engine paint, and actually the parts-store brand is just fine as well.