Yeah, this should be a function IMO. The best thing would perhaps be to pause the entire bot when you are hovering over the active game window, but something as easy as a pause hotkey/button on the client next to "Stop" should also do well. You can press "Stop" in the bot when you want to do things manually, and then "start" when you are ready again, but for some reason this occasionally clicks on End turn the moment I press stop. Usually with no mana spent and several cards on hand. This causes me to lose the game more often than not, so I refrain from doing manual move most of the time.