You can't reprogram the timers in the 2007 and 2008 MasterCraft boats. They came with a maximum run time of 6 minutes. You need to replace the timer modules with the newer
Mastercraft Ballast Pump 20 Minute Timer Modules. They have a max time of 20 minutes but you can program them for as much time as you need. I have placed a link to the toggle instructions below. You might be able to get a little more time out of your system than what you have now but it will be maxed out before the bag is full.
MasterCraft added the newer timers in 2009. Before 2007 the system drained above the water line so the timers were not needed. The driver had both an audible and visual indication of when the bags were both full and empty.
MasterCraft Jabsco Pump Timer Instructions