Sorry...could you clarify for me?
You cleaned and removed his scent from the litterbox is what I am understanding...
You definately want to leave his scent in the box!
If he is new to littertraining he will need the scent to find and be encouraged use the box!
Try cleaning upanymesses outside the box with a Kleenex and then putting the dirty Kleenex in the litterbox where it should go...
If you notice there is a particular area where he chooses to go...move the litterbox to that area, once he gets the litter idea...you can slowly move it to where YOU want it...
Make sure not to go too crazy keeping the litterbox clean right away...make sure it smells like him...leave it "dirty" for a few days so he can find it! Just keep moving the Kleenexs with the urine to the litterbox for him...
Un-neutered males feel the need to mark their territory...other than cleaning it up as I mentioned above and making a point of putting where it should go...you will need to get him neutered to see a definate difference!
I hope some of this helps!
Danielle