you don't need worry about it, and you don't need worry about his words with the check. Your relashionship with him is bound by your lease, so anything else, except that you write in paper, will not be valid.
Just sent a signature-required letter /email (be sure he will received) to him and tell him his request will not be acceped, but the check will deposit as the rent according to the lease. If he deducted the rent for any of his reason, you will charge late fee, ....
If he keeps deducting , then you can start eviction.
Never allow tenant deducts anything from the rent
