I use potty pads with Harley and I can't smell them at all. Now that he doesn't go so often (he is 7.5 months) I put down a fresh pad every morning. When he was younger, I would usually change it twice a day. I too flush any poop and just take the pad out to the trash with the normal household trash. I have been looking into washable pads, but have only seen the ones they sell at PetSmart in person and those seem awful rough to me!
Jeri and Harley