How do I enter my online contribution processor's transaction fees?

Enter the full amount of the contribution that was authorized by the donor, including the transaction fee using the Monetary Contribution function under Contributions.

Then you should enter the transaction fee as an expense paid to the vendor using the Monetary Expenditures function under Expenditures. Your C-3 will not match your deposit slip for this contribution so you should keep a note regarding the discrepancy in your campaign records.