I wouldn't worry about the spots.

I've no idea what you need tea for. Where's that idea from?

Changing the water in the base is really a "make it up as you go" kind of thing. If it looks to be turning murky I would change the whole volume out.

You don't need to cycle the water in the water feature unless you're keeping fish in it (bad idea). The water section is really for drainage, not much else. Any "filtration" is done by the substrate as moisture passes down through it.