Hi,
you don't need to worry about the earth at all. Your main concern should be the stabilityof your ground level when you have multiple power wources.
The key issue in your case is to keep the signal levels in the same level. By having a good ground signal, you make sure that the 5 volt on the output of your FPGA is the same as 5 V on the input side, since they both have the same reference point.
If your application is an industrial application, I would recomend to use a transzorb on all the output signals the value of the transzorb should be at leasr 2 times the maximum voltage. If you do so, add a small 0.1-5 ohm resistor to your output signals that will work as fuses for your device in case you get a nasty big spike, the transzorb will be activated and the resistor will burn, but the rest of your devices wil be OK (I used to work with 3000 volt control of devices using Xilinx XC4005 FPGAs).
Hope you find the information helpfull. May I ask if this is a school project, a hubby project or for a device?
BR,
/Farhad