My Boss is annoyed by delivering many Recommendation Letters

I think that can work, though admittedly I have very little knowledge of how the process looks on the recommender end.

For all the schools I applied to, I had to fill out the recommender's email address in my application and the form was automatically sent to them. What I'm guessing happens (and someone else, please chime in if I'm wrong) is that the recommender then has to upload the completed file to the link for your application that the email provides. So essentially, they could either fill out the form or attach a standard letter instead, as long as it met the file criteria (PDF, Word, etc.)

I would suggest trying to decide on your top choice school and making sure that if it's going to be 1 letter for everywhere at least it is tailored to your top choice school's questions.

You probably know this, just want to be clear, but the rec will have to be sent from your boss' email address. So even if he sends one scanned recommendation (don't know why it would be scanned, couldn't he just send a word doc?), it must come from his email address. You can't send it for him.

Agree with Mappleby, I would either do that, or find the most comprehensive set of recommendation questions for the schools you are applying to and make sure he addresses all of those. At least then he's touching on a lot areas that are of interest to the schools. Another thing I would say, is to perhaps give him some pointers on things he can mention. Remind him of your work achievements and let him know what sort of qualities you want him to discuss that you possess. The guidance will make the process easier for him, and ensure that he writes something that is good for you!

My previous manager also simply submitted the same letter to each school (he actually snail mailed it first, because he claimed they would take the letter more seriously... I had to convince him to upload the letter of rec instead...) Either way, he showed me the letter at some point, and it was great (glowing) but did not follow any of the schools formats... I still got interviews/got in... So it may not matter THAT much

This is correct. Just see if your boss is willing to copy and paste the same letter in a few places... Give him all the info together, so he can do it all at once.