Sorry if I was confusing. I though the EEPROM write limit was closer to 1000 so that's good to know.
I was asking if I need to directly modify the values in the firmware (Marlin) and flash the modified firmware to the board so theoretically the correct values will be there by default.
When it is all disconnected and powered off, when I power it back on, connect, and go to the firmware window all of the values (steps per mm, speeds, acceleration) are blank. When a value is blank or incorrctly typed the text area turns red is what I meant.Even after I click to read from the board the values still stay empty. They don't show up until I hit the reset button on the board then the values that show up are the default.
I believe it is using the default when I can't see the values because the PID on the bed seems to make it take much longer to heat up compared to when I enter its calibrated PID settings in. But I may be wrong on this.
Essentially, I don't want to keep up the repetitive task of re-entering the values for my printer each time I power it on, or I want to know if the correct setting are in there even though Repetier can't read them.