I think that I can offer you a bit of help. This year is my first time applying and using interfolio, but I have successfully uploaded all of my letters to interfolio and all have been received by AMCAS so I can at least speak for the MD route (although I imagine it is similar for AACOMAS). When you ask somebody to write you a letter of recommendation that will be uploaded to Interfolio, you have two options:
1) Send them an electronic letter request to their e-mail address through interfolio which gives them instructions on how to upload said letter to interfolio
2) Give them a hard copy letter request that can be printed off from interfolio that gives them the same instructions about how to upload their letter.
Once they have received the letter request, the only thing that you have to do is to wait and hope that they will finish your letter in a respectable timetable.
Once they have sent their LOR and it is received by interfolio, you should receive e-mail conformation that interfolio got it. At this point, you can send the letter off to AMCAS or AACOMAS. To do this, you will click on the document on the manage documents screen and select start delivery. From here you just follow the instructions of what to do. They will ask you where you want the letter to be sent at the top so just type in AMCAS or AACOMAS and the address should pop up. From here you will need to enter your AMCAS or AACOMAS ID #, and they will also ask for the letter ID # from AMCAS or AACOMAS. To get the letter # from AMCAS or AACOMAS you need to create a letter request in your primary application and each entry should have its own unique ID #. After this you should be set!
Let me know if you have any more questions, hopefully this helps!