How to disable Better Touch Tool (BTT) inside a specific app?
Click on BTT's menu bar icon, and then select Disable BTT for Current App.

To disable specific global actions inside a specific app, do this:


Open BTT and make an action for what you want to prevent. For example, you have a global shortcut ⌘+F which perhaps opens Alfred, but you don't want it to happen in the Finder. In that case create a new BTT gesture in the Finder and set the trigger to ⌘+F.
Then set the action (which happens if you invoke this trigger) to simulate the shortcut ⌘+F. Essentially you are remapping the shortcut to itself, because per-app shortcuts take priority over global shortcuts.