The Amount field is for purchases (event tickets, goods, services, etc.)
If the Enable Donation option is ticked, there will be the option to an additional donation on top the purchase amount.
The Total Amount is the combination of the Amount and Donation. The Banked Amount should be the same as the Total Amount.
If the Payment Form Type is set to Donation, any payments will be inputed into the Donation Field.
For understanding how Total Amount on the Payment Txn relates to Total Paid on the Opportunity, see: What is the difference between Total Amount, Total Amount Charged, and Total Paid?