If you have an IMAP, Exchange, Office 365 or iCloud account you carnt normally stop server mail synching to the client (apart from POP account checking when eM Client starts up in Settings & in the account General tab) unless you either “disable that mail folder on the server end” or “disable synching specific folders in the client” or “hide the account completely” in the client.
So if you want to disable server mail folder synching in eM Client and have an eg: IMAP account see @Gary post below in the following thread how you can do that for specific folders.