On all of my commonapp colleges, I have one academic recommender assigned and one supplemental recommendation (music teacher). However, the music teacher’s recommendation is grouped with the academic teacher recommendations as it was submitted through Naviance. I have a second academic teacher’s recommendation written but it is not yet added to the commonapp (working on this). My concern is that for the colleges that only allow two recommenders (commonapp says “2 allowed”), my second academic recommender will be unable to add theirs due to the supplemental letter being included in the count. Will the website object to my teacher’s letter of rec being added? Time is very limited so I am attempting to clear any complications that may arise in the near future.
Edit: There is a chance that my teacher’s letter of recommendation may be submitted a couple days late. If this does occur, should I contact the colleges about this or just send the letter and not say anything?
I don’t know because I’m trying to figure out the Naviance bit (having never used Naviance before), but for the letter being late, then it probably won’t go through common app because you have to send in you WHOLE application by deadline (which includes questions answered and teacher RECS), so…if your teacher’s recs aren’t done by deadline, my GUESS is that it probably will be too late for it. (Unless there’s a way to send teacher rec in late seperately)
BTW, always to talk to colleges about problems, it shows responsibility (although waiting till last minute isn’t responsible lol). Sitting quietly might earn you criticism if they catch that mistake. Might.
My concerns about my teacher sending the letter of rec are only if it is able to be added before the deadlines. I do intend to send off the commonapps tomorrow if I am unable to get the recommendation and to send the recommendation separately as soon as it is available
The thing that I have been told by someone who deals with private liberal art colleges is that the college will understand if materials are sent late. That means materials that YOU had no dealing with. Why would you be punished if your teacher failed to send it in by the deadline? So don’t worry if she sends it in late. Granted, it should be sent, I was told, 2-4 days late.
So send in your stuff by the deadline. If through Naviance (which is what my school use), my teachers can still submit their materials 
late, of course.