Being a bit of a DIYer, I might personally try a red Sharpie. The safety filter is red after all. I know from experience that a black sharpie is not opaque on film; it smears and won't cover uniformly. You might also consider making an initial print and then cutting out any areas you want to burn in. This then leaves the possible problem of too-obvious edges on the burned in areas. Maybe a smaller print... for example, make a 5x7, cut out your areas to be burned, and then print an 8x10 while holding the 5x7 halfway between the lens and the paper. Of course, you'll need to project the image with the safety filter engaged to line up the 5x7 first.
Just thinking out loud... hopefully something will be helpful. I honestly can't think of anything that would be easy to apply to film that would remain uniformly opaque. Check out some of the bigger photo supply shops online maybe?