Hi. I have a non-immigrant Education (study) visa that's single-entry. I'm here now in Thailand and used my single entry, but I have to leave Thailand for a few weeks and when I return I would like to continue using the remainder of the visa. Do I apply for a re-entry permit at Immigration? When I return to thailand, it will be before the date of my 90-day check-in. Do I have to go back to immigration when I return to check-in also? Can I do all of this in one trip to immigration? Thanks.

Simply ask your school, they will take care of the paper work. Probably will take few weeks. I used to have ED visa for many years, now retirement.

No Dice on the school helping me. I'm not sure this was the best school to go with, but it is what it is. They told me I need to go to immigration to apply and pay for the re-entry permit.

Yes you need a re-entry permit - either from immigration office or at airport prior to departure (after check-in). You enter that information on arrival card (same permitted to stay date you currently have). You do not need to visit immigration after return unless you plan to extend your stay for study and then you would make normal application.