Marlin firmware code is writen and supported by the reprap group, nothing to do with Repetier, however, repetier host will work with marlin firmware.
Repetier firmware is repetier's version of marlin (personally i prefer repetier firmware,its a lot more stable).
Marlin and Repetier have some differences in what G/M codes are used, there is a good wiki on these here
I suspect the firmware you have on your printer is a FLsun doctored version off an old Marlin firmware.
Yes, the Repetier firmware configuration tool will build a complete new repetier firmware (use the 'dev' version)
you will need to know what settings to enter into the tool, like steps/mm for x y z e steppers, thermistor types , type of endstops etc.
Then when finished, download and reprogram your board using the Arduino software
umm, what controller board is used in your printer ? best make sure it is supported before trying to upload to it :)