To allow e-checks to be chosen by users, this is done in the different areas that you set up payments (seen as EFT/Direct Debit).

For example, an Admissions Manager can set this up in Application Forms.
  1. Navigate to Enrollment Management.
  2. Select Admissions > Admissions Setup > Application Forms.
  3. Click Edit to the right of your form.
  4. Click your Payment tab.
  5. Edit the Block Settings of the Payment Block.
  6. Select Yes for Electronic Funds Transfer.
  7. Save.
For Contracts:
  1. Navigate to Enrollment Management.
  2. Select Enrollment > Contracts > Manage Contract Forms.
  3. Click Edit to the right of your form.
  4. Click your Payment/Deposit section.
  5. Select your Payment Gateway.
  6. Turn on Direct Debit.
  7. Save.
Another example is through Giving. As a Giving Manager:
  1. Navigate to School Website . 
  2. Select Content > Giving.
  3. Click the Giving Forms tab.
  4. Edit your Giving Form.
  5. Click the Field Display Properties.
  6. In the Payment section, check off Electronic Funds Transfer.
  7. Save.

There are other areas as well, but as the above directions state, you will just need to edit the payment area of each form or module that is accepting the payment.