[I've never done it. I've had my unit for 3 years, and change the filters every 6 months. I will rinse out the acrylic sumps before reassembly.
I don't like the flavor of DI, so I have a Tee in the line going ot the DI, and collect RO water 1 gallon at a time, about two times a week. We refill small drinking bottles, and put those in the fridge as they are handy that way. We stopped buying nearly as many cokes as we used to, about 6 months ago.
I don't bother using RO water for cooking, coffee, tea, etc... just for drinking.
I've never used the wastewater for anything. It goes down the drain, unseen.
The storage containers we use should be cleaned out with bleach water (1:10), then left to air dry for 24 hours. This will sterilize it of any slime or algae that may be accumulating. If you make a barrel of water and the TDS is high, the container needs to be cleaned thoroughly.
I've no experience with the bladder tanks that some RO systems use, and have no idea how you'd clean those.]