You email him the gerbers. There's no minimum order size. That said, he's one of the nicest people I've interacted with in the hobby community, so I would encourage you to not order like 3 boards or something insignificant like that.
The board is 0.2 square inches. So technically, at a cost of $5 per 3 copies of a 1 sq inch board, the cost for 3 of these PCBs would be $0.90 cents. If you consider that he includes shipping for free, then I think it would be majorly crappy of someone to order $0.90 cents worth of boards. He'd be loosing money for sure (and I'm sure he'd still do it, cause he's pretty awesome). Dorkbot is an awesome resource, but we're definitely getting much smaller sized PCBs than I think his pricing model is designed for, so it's good to make up for it by upping the QTY.
But maybe grab like "6 sets of 3" which would be 18 boards, and would probably cost you $5 to $8 shipped.
Whenever I order from DorkBot, I'm always pretty careful to grab like 30 boards, even if I really just want 1 prototype board done, if it's something really tiny. Like those 8x8mm STCS1 drivers - even 60 of them only came to $10. It would have been pretty unkind of me to have him make me 3.