How do I file a counter claim against my landlord, when I am being sued for non-payment of rent, when he actually owes me money. I do not have an attorney and I can not afford one, so I will be representing myself in court.

Assuming you received a summons, go to the court that issued the summons and ask how and whether you can file a counter claim. You may have to go to a different court (small claims court) to do so.