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How to implement a verification system
There are more options to make EmpyManager compatibly to a verification system.
Instead of using channel syncing, we suggest to free users to enable Discord's verification system. It is safer than any other bot's system and users won't be able to join channels without being verified.
If none of the above solutions fits you, you can always remove the "View Channel" permissions from @everyone in your server's global settings and then add it only in the channels that non-approved users should be able to see. Then, you should grant the "View Channel" permissions to your Verified role.
In this way, all the non-specified channels (including EmpyManager's channels) will be hidden by default to non-verified users.