Yes, Accelo has so many features that it can be hard to manage the ones you want your team to use. With module deactivation you can simply turn off the modules you aren't using. Say you don't need the retainers module, simply deactivate it from the Admin Dashboard. There's no need to worry about any retainers being lost by the deactivation because Accelo safely stores them in your deployment database until you reactivate retainers again. The admin dashboard is useful for crunching the numbers on how your business is doing as it gives you real-time figures of each module progression.
To configure your modules head to the Configurations then click Manage Account, find the desired module and switch the Status to OFF. If you see in the image below, the module is still active.
Once switched to Off, it should disappear from the main navigation.
There is also a shortcut to configure the statuses and progressions next to the deactivate/activate button.