NOTE: “Single-sided” refers to the design; does it have traces on one or both sides?

If you are using a double sided substrate, such as those provided by The Hive, go back to the PCB fabrication page and run the appropriate two-sided process (i.e. with or without plating). Nothing will change (including the “Double-sided” option in the Process Planning Wizard). The etch should still be done with the double-sided template because the etch will either isolate the holes on the back-side if you’ve made a bottom-side copper pour/polygon, OR it’ll etch away the entire backside. (Why? Otherwise anything put through the holes may short because of the copper on the backside.) So really, nothing changes at all from the standard double-sided process.

If you have a single sided substrate, meaning copper on only one side, go back to the PCB fabrication page and run the appropriate two-sided process (i.e. with or without plating). Note the following:

• In the ProtoMat setup, in the Process Planning Wizard (button #1), for “Substrate layers”, select “Double sided” as you would for a standard double-sided process. If you don’t, it won’t stop to let you etch before it cuts the board out, and then you'll have to start over since you can't etch safely once you've cut the board out.
• You will use a single-sided ProtoLaser template (either top or bottom, depending on where your traces are). Make sure the “Supported by ProtoMat” box is checked in the template window, or else it will try to drill the holes on its own.