The short answer is, yes you can bill outside of the Fons system. You can do this by setting a client's rate to $0 inside of Fons, and when you send them an appointment invitation you can simply add a message to it requesting payment through their preferred method.
That being said, Fons exists to automate all the admin for a business owner. This is why we encourage your clients to switch to automated payments in the Fons system.
For clients who want to pay with check, you can tell them that we accept ACH payments! This is the same thing as a check since it pulls money directly out of a client's bank account the same way a check does.
If their payment info is entered in their Fons account, you won't have to remind them to pay (we do that for you) or hunt them down for their payment (we do that for you) or enforce your cancellation policy (we do that for you!)