Can I charge a percentage fee on the order (e.g. 3% COD)?

Not as a true percentage line item. Fees tied to cart total must use flat amounts, typically on a shipping rate with order-amount tiers. Payflow’s percentage-to-tiers calculator (in the Help center and Cash on Delivery (COD) Setup) helps you build tier rows that approximate a target percentage — for most stores that is enough in practice.

Payflow Pro unlocks unlimited active customizations when you outgrow the free allowance (one active at a time, shared across COD Setup, Payment, and Delivery). Heavier setups (for example several payment customizations for different checkout paths) need those extra slots.