We have multiple transactions for one EIN that together require a CTR. The problem is that they have multiple names under that EIN. For example, there might be a checking labeled "Rock Island School District" and another checking account labeled "Booster Club" and a couple accounts with other titles. They are all under the same EIN. What would I put for Section A?

The entity's legal name should appear. Titles like "booster club" are just courtesy titling for the customer.

While you're working on this, check out the "Booster Club." It's probably an informal organization that somehow convinced your bank to open an account for them using the school district's EIN, without authorization. That organization should have its own EIN and you should probably get someone in your bank to start chasing them for it.