I know what you mean about the e-collar "getting in the way" lol. Our poor girl bumped into walls, knocked over lamps,etc.
We kept it on her MOST of the time. If we were able to keep a very close eye on her than we would remove it for short periods of time to give her a little break.....although I don't know if it bothered her as much as it did us
We did, however, cut it back a little so that it was easier for her to eat/drink but so that she still couldn't reach her stitches.
As far as the pain, our vet had prescribed some pain medication. I tried to only give it to her at night so she could sleep better. Our girl only seemed to be "uncomfortable" for the first few days.
Best wishes to your boy for a speedy recovery