When sewing other stuff (home goods, garments), I just left that part till the end because most things would get snipped off in the construction process. But quilts have a lot more threads! Finally, on the last one (of the few I've made), I trimmed them all as I went along -- pieces, rows, quilting lines, the works. Much easier!
If I have ends I want to run in instead of snipping, I'll mark those with a little safety pin so I don't miss them later.