FT5 should be running marlin firmware. This by default should have EEPROM (a form of quick easy access programmable memory) disabled. This is for a very valid reason as people can often forget that they have saved EEPROM values which under normal use override firmware values.
With EEPROM disabled you will need to do a PID tune and manually edit the firmware and upload this.. You can use something Repetier-Host to complete the PID tune and then upload via arduino sketch.
Here are some links for you.
If you get super stuck I can modify the stock firmware file for the FT5 if you are able to give me your hotend PID values.
The PID values will alter how your hotend responds to the environment ie; how fast it responds to temperature change, how much overshoot and how aggressively to stick to target temperature.