Teacher Recommendations and Supplements

<p>I'm pretty confused on how the whole teacher recommendation process works with common app.
I'm planning on sending two teacher recommendations, one counselor recommendation, and a supplemental recommendation from a research mentor.
Some of the schools that I'm applying to require two teacher recs while others require only one.
In that case, would I send both the research mentor rec and one of the teacher recs as supplements?
Also, how will my supplemental recommender send her rec?
Will she have to physically send the rec to the school?
My school uses naviance, so I'm wondering if I could just go ahead and add her name on my list of recommenders on naviance and then tell my counselor which schools don't allow more than 3 recs.
I'm kind of lost in general, so any help/advice would be greatly appreciated!!</p>