How to put polyurethane on wood, one side at a time
Doesn't make any difference, really; the question is number of coats per surface, not order they're applied in.

The thing to watch out for is that there will be a tendency for drips to run down the edges and onto the other face. You may want to use masking tape or other techniques to guard against that, though going with multiple thin coats rather than fewer thick coats will also help (and is the better practice in any case).

(This is one advantage of HVLP spray&mdash;the atomized finish dries almost on contact, so it doesn't tend to run unless you seriously over-apply it.)