I intend to do a little work to my car eventually, but a friend of mine needs to know for his car too. When side skirts are installed (not moulded) should the car be sandblasted, then primered/painted/clear coated THEN put the skirt on and paint the skirt, or some other method?

Parts should always be painted separately, and then installed, you get much better/cleaner results that way.

So in your case, if you were to paint the whole car as well, you would test fit the parts, drill the holes, paint everything separatly, then assemble.

then just touch up the spots where the resin/body filler would fill the holes for the screws?

I am not sure I follow your question.

You would perform all your body work, repairing, etc.
Afterwards, you would test fit your skirts and mark the holes on the lower rocker panels and door, then drill them.
Once that is done, and you know the holes line up with the mounting clips for the skirts, then you paint everything, the paint will give a nice clean finish around the drilled holes, thus protecting any exposed metal, and then reassemble.

If you wanted to, you could put some silicone adhesive (like permatex blue) on the mounting clips before snapping them into the drilled holes.
This would provide a really nice, strong and pretty much corrosion proof bond.

so the side skirts just "pop" into the holes? you don't generally have screws that run all the way through the skirt?

There are screws that mount the lower edge of the skirts to the rocker panels, those are easy to drill.

The rest of the clips are plastic and they snap into place in little retainers that are molded to the inside of the skirts.
You have to then match up where the the plastic clips sit on the skirt, and where to drill the appropriate holes in the body.

When you go to install the skirts, you have the plastic clips in the skirt, then you just tap them into the drilled holes, install the screws on the lower edge of the skirt, and you're done.

Gotcha, I understand it now. Thanks a ton Dan