The data in your cryptomator app is accessed directly on your cloud. So all you have to do is to put the files into the cryptomator app and your selected vault. Then they are stored encrypted and online.
You need to sync all encrypted files to you desktop eg via google backup and sync app. Then you’ll have to install Cryptomator, ad an existing vault, and select the masterkey file that you find in you local vault-folder.
Please read here: Why is the masterkey stored in the cloud?