Which spokes go on the non drive side and which go drive side? I just wanted to make sure I understood the guy at the shop.

The spoke calculator gives you left side and right side spokes lengths

Left side go on the non drive side i.e. the side where the rotor is, right side goes on drive side i.e. the side the free hub body is on, yes?

Just out of curiosity what would happen if you got them the wrong way round? Are there signs that suggest you have done so?
Yes, right side is the drive side. Assuming that both sides use the same "cross" arrangement the shorter spokes go on the drive side of the rear wheel, so that the offset due to the drive mechanism will be compensated for and the wheel will be centered.

If you swapped the L/R spokes, the drive side spokes would be to long and the non drive side spokes would be too short.

Note that if your spokes and spoke lengths are the same for both sizes this won't matter, of course.