When I use to do a lot of plug pulling I would mark the 50 & 60' marks on my reels with different bobber stop knots. I would suggest using dacron because it comes in different colors. Also fly line backing works well too.

If you want a plug to run like a fine tuned watch tie a perfection loop to the eye instead of using clips. I agree it's a hastle but it works outstanding!

Good Luck!