As a freelancer, you pay the fee on all earnings, including bonuses. The fee is included in the amounts clients see on your proposals, contracts, and profile. Most of your reports show only total charges, inclusive of the fee—the same as what the client would see.
Your fee is listed as line items in your Transaction and invoices report and your Billings and earnings report. The total billed to your clients is considered your income, and the fee paid may be deductible as business expenses.