I've always scribed them in next to the raised panel line. I'm not going to lie, it kinda sucks and takes a lot of work..., but I'd rather do that than have to worry about losing the raised lines when filling in seams and things like that. After scribing the Monogram 1/48 scale B-25 and the F-101 I've become pretty good and quick at it.
To repair, stretched sprue does work pretty good but I have always had difficulties trying to get it to match up properly, and I still ended up doing a bunch of sanding to make it look right.
I've read from a few sources that most of the raised panel lines are out of scale and need to be toned down, but I guess you could say the same for scribed lines as well.