The most important thing to check is that all your readers and writers are supported on the Linux platform, which is what is used on FME Cloud:

https://www.safe.com/fme/formats-matrix/#platforms

Other than that, you should consider creating a separate FME Cloud instance for testing purposes and try out the workspaces there before migrating to the live instance.

Another consideration is where your data lives. If FME Clouds needs to connect to on prem datasets that would introduce a lot of data transfer back and forth as well as IT security measures.