I'm not sure if you can or not but would agree that it should be implemented the same way they let you auto progress the players. I know I left the scouting points untouched until about mid way through the season until I found out that unused scouting points don't roll over from week to week, so started throwing the points at FS and OTs just cuz they are my weak spots.
Ideally, would much prefer the scouting be set up similar to the NBA 2K GM Mode where you advise your scouts on what positions to look at, and at what depth (blue chippers, mid rounder, late-UDFAs) and whether to invest future scouting points on a prospect (scout = ceiling is low but immediate contributor, etc.)
Not sure of how this will impact the draft at all; hope you're not left completely in the dark when drafting if scouting points aren't used at all which would be gip. I would prefer they moved all the scouting to the off season as it makes it too meticulous and tedious to want to perform on a weekly basis.