Hi @KeriSalyards,
In he scenario you're describing, where courses are all created in one account (I'll say Account A) and then you move them to different accounts later (Account B, C, D, etc), the only template that would get applied automatically to the courses would be the template set up for Account A. If Account B, C, D have their own templates, you'd have to basically do an import of that template course into each course manually (you could perhaps use some scripting/APIs to try to reduce workload if you're familiar with programming). I don't really know any other alternative methods for doing this...
As you already seem to know, your SIS would ideally put everything in the right place to being with, but you said that's out of the question due to cost right now. It may be worth having more conversations about that in the future though, as I'm sure doing all of the work manually is going to take you a significant amount of time, and time does equal money too!
-Chris