sure, you need to set where the encoder position is. What I would do I would check what is stroke limit ( system machine parameter, not user or software limits ) and set the system position according that limit - to have the axis position more less logical. After that it should be possible to move the axis in manual mode and set system limits. The next are software limits. The next - user zero.
Can't tell if the machine system limits are easy to set like other parameters ( CALL ), however. Maybe assistance of local Okuma representative is required.