I don't use a 1/4" foot with my machine, but I know what you mean. I have a ruler that has black markings on it and they can be difficult to see when using black fabric...which I use quite a bit of.
If this were me, I wouldn't use the nail polish. I'm a big enough of a klutz that I'd get it everywhere. I personally would try one of those White-Out pens to make the mark.