The short answer is yes.
Frooition support all payment methods allowed on your eBay site, including 'managed payments'.
There is nothing that you need to change in the Frooition software in order to have managed payments in eBay.
Here is a link to some more info on managed payments: https://secureir.ebaystatic.com/cr/v/c1/dlp/PDF%20checklist/uk_MPchecklist-a4-v3-1.pdf
If you have any further questions on this issue, please contact our support team.