You can choose either method. If you open the SyncToy application you can create folder pairs to sync whenever, you manually click the "Run" button. Or once you have created the folder pair you can add a scheduler to run a sync of that folder pair. For example you might create a scheduler that runs a folder pair called "Browser Favorites" as follows:
SyncToyCmd.exe -R"Browser Favorites"
For more details on setting up a schedule task check out the SyncToy help under the topic "Schedule SyncToy"