When you connect Meta, the platform lets you add a fee: that's where you enter the percentage they charge on your total spend. That fee is treated as a fee and is included in your ad metrics.
What isn't possible
A fee calculated on revenue attributed to Meta, that is, a percentage of sales instead of spend. If that's how your agreement with the agency works, message us: we'll give you the numbers so you can add it as an additional cost with the real amount.
An additional cost also has the add to ad spend switch. Turn it on only if that expense is advertising: it makes the cost affect ROAS and True ROAS. If it's rent, salaries or your accountant, it should stay off or it will distort all your ad metrics.