Have you tried putting two litter boxes in the cage.  Or put sheets or old
shirts in the areas he is going to the bathroom.  I had a ferret that was
the same way and I just kept taking her everytime I saw her starting to go
to the bathroom grab her and put her in the box, then give her a treat.
The people I got mine from just filled the bottom of the cage up with
litter so I had to train them.  I was able to get them trained in just a
couple of weeks.  Have you tried the big retangled litter boxes.  They
work good for 2 ferrets they are able to have more room.  I hope this
might help you.
 
Diane, Ruby & Lexi
[Posted in FML issue 3575]