Many people don't use squeegees because they can cause scratches. You might want to consider ditching yours if you're running into scratches as a result; just hang the negatives to dry after a dunk in Photo Flo and/or a spray with distilled water. Personally, I get drying marks when I do this, so I'm still (cautiously) using a squeegee....
As to your existing question, there are ways to deal with scratches, particularly if they're on the base (non-emulsion) side of the negative. One is to use oil from the sides of your nose; lay down a thin layer and it should enter the scratch and even things out, making it possible to print without seeing the scratch. If you prefer to keep bodily secretions off your negatives, you can buy scratch-hiding fluids. I've used one of these (called Hide-a-Scratch, IIRC) and it works wonders, at least for scratches that are on the base side of the film -- I've never tried it with scratches in the emulsion itself, but I suspect it wouldn't be very effective for those. In either case (nose oil or a commercial product), you should wash away the scratch-hiding substance after you've printed the negative. I use PEC-12 and PEC pads for this purpose.