Well GPS is part of the system, its integrated by whatever means you chose the system to be designed, I am guessing either you have a computer with I/O DAQ for the Fly-by-Wire and serial or USB or Blutooth GPS input. The more advanced and old-school people may have TTL or something else going into their system. Then you have to worry about shielding from EMP if its a fighter jet, interference it may cause to other electronics, mechanical tests to see if the system can withstand the environmental stresses of temperature, humidity, pressure, electromagnetic interference, any possible short circuits that could ignite the wiring, any overload issues, etc.
I'm sure a MechE could find something to spend time looking into.
I'm not familiar with satellite computers. If you are referring to satellite communication systems then that's Electrical Engineering. If you are referring to motherboards, firmware writing, and peripheral accessories for computers, then that's still EE or Computer Engineering. Its mostly all EE for the hardware, and Computer Science for the software.