On the recurring Payment, there is a lookup to the Payment Form.  On the Payment Form, there is a field called "Payment Type".

When the "Payment Type" has a value of "Donation" then the "Donation Amount" field is updated / used.

When the "Payment Type" is NOT "Donation", then generally the "Payment Amount" field is used.  If the "Enabled Donation with" is enabled on the "Payment Form", then the user is asked if they wish to make a donation as well.  In this case, the "Payment Amount" and "Donation Amount" will both have a value.  An example of this being used is for a membership where the member is also prompted for a donation with their membership.

The amount charged is the sum of "Payment Amount", plus "Donation Amount", plus any applicable surcharges.