The only worms that are transmitted via fleas are tapeworms. All other parasites come from the dirt and/or contact from other animals that have them. You need to use a dewormer containing pyrantal pamoate to ensure hook and round worms are both killed. You need to treat every pet in the household - and retreat in about 14 days to kill any parasites that hatch after the initial dose. If you don't treat everyone at the same time, they will keep passing them back and forth through the litter box. If the cats go outside, they will also continue to possibly get them.
As far as him not using the litter box, you need one litter box per cat plus one extra. Try using a new litter that is out called Cat Attract Cat Litter. It has been a life saver for me and one of my girls that never used the box. She hs been perfect since using it. Make sure you clean all soiled arease with an enzymatic cleaner designed specifically for cat urine such as Zero Odor or Natures Miracle.
Please let me know if I can help further.