I'm not positive, but from looking at the AM site, it looks like there's an output shaft on the black plastic side of the
toughbox mini, that is meant to have a
US Digital E4P encoder mounted to it.
I can't tell for sure from the pictures, but it looks like there may be screw holes in the plastic of the toughbox mini for the encoder to be mounted to.
This method of mountign seems to be consistent with how it's done on the
CIMple box from AM.
Also from lookign at assembly images, it looks like the encoder output shaft is actually the back end of the output shaft of the gearbox itself. So that should help you locate it, and it also means that your encoder to gearbox output ratio is 1:1.