We have a customer who deposited money into an individual account and into a UTMA account. Currently I have the minor's info in Section A and the custodian's info in section B with both accounts listed in item #35. Is this correct?

If I understand you correctly, the custodian made a deposit on his/her own behalf, as well as a deposit to the minor's account. As such, you will need to check Multiple Persons at the top, list the custodian (since he/she owns the individual account) in section A, then check box e- conducted on own behalf in section B. Then, on the second page, complete section A for the minor.

Jac is right on the money, that is how I would fill out the CTR.

What do you use for Box 14 on the CTR (Identification) for a Minor? He does not have a driver's license.

Since the minor did not conduct the transaction - enter N/A:

Item 14. If an Individual, Describe Method Used To
Verify Identify. If an individual conducts the
transaction(s) on his/her own behalf, his/her identity must
be verified by examination of an acceptable document
(see General Instructions). For example, check box a if
a driver’s license is used to verify an individual’s identity,
and enter the state that issued the license and the number
in items e and f. If the transaction is conducted by an
individual on behalf of another individual not present
or on behalf of an entity, enter N/A in Item 14.