Duet is not 100% due compatible. It uses pins not defined in due and the sd card uses parallel mode not spi mode, which is the only mode supported in repetier. Also there is no ethernet support in repetier.
So with a patched due variant you can use it with new pin definition if you don't use sd card and ethernet I guess. In reprap forum->Repetier is a discussion with the developer where he shows the missing parts if you are interested.