You can choose the folder that is used for synchronization with Bitrix24 Drive. Just right-click the Bitrix24 Desktop app icon at the bottom right corner > click the cogwheel button.
Then select the Bitrix24 account you want to configure synchronization for (if you use several Bitrix24 accounts in the Desktop app) > click Settings > select a folder you want to use for synchronization.
In such a way, you can select different folders that will be used for synchronization with different Bitrix24 accounts.