Only always rinse any filter media with pwc
or treated water. For your filter pads only if it is weirdly gunky, just leave if most likely. Save the BB!
Are you ditching / tossing the other substrate rocks?
If so then use a store mesh media bag or 2, or the tightly netted garlic, citrus or veggie bags wash well, which can contain the stones and use a couple bags in the back for a few weeks. I hang them vertically next to the filter out flow and intake.
Doesn't look fabulous but keeps the fish well. Even used to keep one behind some plants so if I ever got a new tank to set up I could pull it right out for the job.
The stones have a good amount of BB also, and can help with the cycle.
As an example if you remove the substrate in a tank to change it to something else it pretty much always causes a mini cycle because of the BB in the substrate helping to maintain the necessary BB to handle the tank waste.