A Collection of Questions on Letters of Recommendation

I’m currently a senior applying for colleges, and I’ve already sent some of my applications (and requested my letters of recommendation from teachers- and registered them in Naviance). In the process, I realized I never filled anything out about my recommendations for each college (I’m using both Common App and Wisconsin Admissions Online), besides signing off my FERPA rights. After some crazed panicking, I found that recommendations can be sent after you apply, electronically even (via Naviance and guidance councilor). And while that’s nice and good and all, I still have one other question.

How do I select which recommendations go where?
-some of my schools only allow one, while others allow two, how do i select which one?

Sorry if this should be obvious… but I think the “deadlines due this Saturday” stress is getting to me!
Thanks you in advance for any light you can shed on the matter!