1st, let me say that I am not an expert. I am self taught by research, mistakes and a lot of questions.
What filler do you use for bodywork?
I use epoxy mixed with microspheres for the big jobs. The microspheres can leave pin holes when sanded. I use bondo for very light body work filling in those pin holes. Sand with 150, 220, spray primer, wet sand 600 spray paint. I've not done any "nice" jobs, but they look good in pictures. I use cheap paints and the work needs to be redone in about 2 years. I usually modify something in that time so I've never bothered with more expensive paints.
Do you use gelcoat to reshoot a ski?
Pat from FGCI told me not to use gelcoat to repaint a ski. He said it is poly based and will not stick properly.
do you sand the ski down to fiberglass or just scuff up the paint and layer over that?
If you glass to the paint, your job is only as strong as the bond of the old paint to the old fiberglass. It is best to sand to bare SMC/glass. Sand to bare glass, prep with 80 grit and acetone.
For painting, yes, you can paint over the old gelcoat or paint if the paint is in good condition. The quality of your result will be based upon the quality of your prep work.