It does sound like you need to play with the fuel timers some more.
The fuel timers start when you take off, automatically, and have since they were released in September. They can warn you every X minutes, or even better, every X gallons, since what you really want to know is imbalance, not just time.
The count up/down timers are really for IFR ops or other things that aren't fuel related. What are you using the timer for that you want it to start on engine start, if not for fuel? The more we know how it's used, the better we can implement a feature.