Non PharmCAS: You have go through a whole separate application. I believe that the majority of non-pharmcas schools require LOR writers to submit their letters via online but you need to double check with each school.
PharmCAS: It all depends on schools that you're applying to...
For example, some schools require letters from pharmacist while some don't. If XXX pharmacy school requires a letter from a pharmacist, and a letter from a science professor. You submit a letter a from a pharmacist, a letter from your chemistry class, and a letter from your sociology professor. XXX school will not look at the letter written by your soc professor. If you fail to submit a letter from a pharmacist, they are not even going to look at your application.
Based on my experience, most schools require 1-2 letters from science teachers while recommending a letter from a pharmacist. You can submit more than the required # LORs but if a specific school only requires two LORs then they will only look at 2/x number of submitted LORs.
For example: One school requires a letter from science teacher while lets students to submit two additional letters from anyone other than family members. You submit a letter from your chem teacher, a letter from pharmacist and a letter from your boss. They will definitely look at the letter from chem teacher. They will either randomly or specifically choose. It's totally up to each school...they are not going to read all submitted letters first then choose the best two simply because they don't have the time to read all LORs.
PharmCAS itself has nothing to do with specific # of required LORs. They are just the middleman. If you submit four LORs, then they will send all four LORs to schools. It's up to schools to decide which specific LORs to be looked at. You can't call PharmCAS and ask them "I want LORs from my pharmacist & Science teacher to be sent to UCSF, and LORs from my pharmacist and soc professor to U of Nebraska".
Bottom Line: If you are applying to one school that requires only one LOR and another school that requires two LORs, then you better submit two LORs to PharmCAS because if you only submit one LOR then the second school will consider your application as incomplete. All PharmCAS schools will only accept paperwork that were prepared by PharmCAS.
You can final submit your PharmaCAS application even before having all LORs. Just have them before schools start handing out interview invites.
Then again, I could be wrong. I certainly don't have the best answer here so your best bet is to check with schools that you are applying to and go from there.
I don't know the names of schools that will not look at your application if you have more than the required # of LORs.
