Once I'm ready to buy a new Stick, do I pay all up front, or do I pay a deposit and the rest when it's ready to be shipped?

You pay a deposit for SE to start the build. I think it's around $300-500. Full payment is due upon completion. Or you can pay in whatever increments you want via PayPal.

After you place the order you get contacted by SE. The details are confirmed. Then you need to pay a deposit to make the order official & get it in the queue. The balance comes due once the instrument is ready.

Edit to add: Brian posted while I was writing the above, my reply is pretty much the same but as I'd already written it I'll still post.