Here are some possible options:
Option 1 - Customer enrolls with a coupon code
You can give the customer a coupon code for either a portion (whatever portion they are wanting to pay with one payment method). For example, if they are splitting the payment in half, the coupon code would be for 50% off. That way they can enroll and pay half.
Then after they enroll, you can take off the coupon code so they owe the remaining half. You can cover this in a few ways:
You can add a second payer if the payer is paying with the same payment method (i.e. credit card) that the customer paid with when enrolling. In doing so, you can then charge the second payer for the other half tuition.
If the second payer is paying with a different payment method (say the customer paid with a credit card and the second payer is paying with ACH) then you can either add the second payer's payment method to the account and charge them the other half tuition or you can have them log in to the account and make a payment there (if they are given access by the primary account holder).
Option 2 - Admin enrolls customer
You can also enroll the person yourself as an admin user and create an invoice. The customer can then pay part of the invoice with the second payer's payment method. Then pay the other part with their own and save that payment method on the account.