Hi, glad you find it useful!
Yes, when renewal happens you will indeed have to update the .pem file and .key you are using.
You should check out the Scripting option (Show Advanced Options) and also check out other pem file questions on this forum such as this: Filezilla Server PS Script
The next major release (which will be in beta soon) will have new deployment options which export .pem/.key etc to the location of your choice, which will mostly remove the need for scripting.