I have been waiting to get a fecal sample done, I probably will do it tomorrow (My guy has been busy) but I'm fairly certain that my bearded dragon has been sick, possibly parasites or something. So yesterday I in depth cleaned the tank and everything inside. It's like a whole brand new setup honestly; it couldn't be much better then it is right now. Anyway, I don't want to neglect it as bad as I did this time, so aside from removing all the poop, and cleaning those spots as soon as possible - how often should I take the tiles out, clean them, soak the branches, etc?
It really depends how dirty it gets. I clean up poops as soon as I see them, and I vacuum out the tank every night, mostly cos I want to get rid of left over crickets, but i also get up any greens they've kicked about the place and any shed skin and other random bits, so it's pretty much totally clean every night. The plastic hide gets scrubbed about once a week, and the wooden branch every few weeks, and the tank itself gets fully scrubbed out every week or so. Once I stop feeding crickets I won't have to worry about leaving escaped live food in there overnight as much, so I probably won't vacuum it out every night, but I will get the poops as soon as I notice.
If your beardie has a parasite you'll have to step up your cleaning routine until the parasite is gone, or he'll just reinfect himself. If it's coccidia, you'll need to do a lot of cleaning or steaming on a daily basis to prevent reinfection, some other parasites are easier to kill and you'll just have to be very quick at picking up the poop and cleaning anything the poop touched.
I don't know about avoiding parasites, but I clean the tank with a bleach solution once a month including all the items in the tank. The feces are removed from the tile I have down on a daily basis. The water bowl is cleaned maybe once every 3 days; it is filled daily though I have never seen him drink from it.