From the equity website:
"Candidates must complete 50 creditable weeks of work at any of the participating theatres. The weeks do not have to be consecutive, and may be accumulated over any length of time."
I signed up from the program after freshman year of college and started working towards my 50 weeks. In all reality I reached the weeks by the end of my junior year. Once you reach the 50 weeks you have 5 years to join equity. After the 5 years you will lose the registration money and, if you were for some reason to start the program again you would have to start from the beginning.
Equity does say that once you have the 50 weeks you can only work at an equity theatre under an actual equity contract. But there is nothing saying that you can no longer SM/ASM a non-equity show, only that you can't work at an equity theatre as a non-eq.
There is a backwards way of still being able to work at an equity theatre as a non-eq that equity would frown upon:
Theaters that participate in the EMC program do not send all of the interns/etc to equity in case they might be an EMC member; you are responsible for getting the weeks submitted (by filling out a form and having the theatre send it it). If one happened to know that they would reach the 50 weeks with a certain job but also know that they are not ready to become equity they would simply have to not fill out the form. You can also backlog the weeks, so even after the show that you PAed/interned/etc on is over you can have the company fill out said form and send it in.
IMHO the emc program doesn't serve that much purpose besides getting $100 towards your card (which was the big perk for me) and possibly showing future employers that you are planning on stage managing professionally (especially if your resume has a lot of general theatre work).
AEA has a lot of answers on their website:
http://www.actorsequity.org/membership/emc.asp