Starting with UPDD Commander 1.6.0, it is possible to configure it to interact with other UPDD client applications such that only desired gestures will control the client application, while other gestures will still be handled by Commander itself.
The first step is to add the application into the application list. Then, there are two ways to proceed depending on whether the app will handle all touches on its own or just certain gestures.
The client application handles all touches
If the application is expecting to handle all touches and you don't want Commander to perform any gesture processing for touches that fall within the app, then you can simply add the "Pass all touches to UPDD client app" gesture:
That will override all other gestures, and no further configuration for the app is required.
Maintaining gesture processing with the client application
If you want some gesture processing with the client application, then edit its gestures so that some of them are configured to the action "Pass touches to UPDD client app". When performing gestures assigned to that action, touches will be received and processed by the client application. Note that there may be a slight delay (usually in the order of tens of milliseconds) for Commander to detect the gesture before the client application will receive the touches.
If the gestures are inherited, then you need to add them directly to
the application before you can change their action. (A shortcut for this is to double click the inherited
gesture.)
This way some gestures can retain their functionality, for
example default gestures used for showing the Notification Center or
the Smart Magnifier, while other touches will be processed by the
application itself. In this case, you can either set the application not
to inherit gestures from "Default Gestures" as described above and then create only the
set of gestures you want to apply to this application, or set it to keep
inheriting gestures, but add the gestures you want to only be handled by
the application and set their action to "Pass touches to UPDD client app". This way, the
gestures defined for the application itself will override Default
Gestures.