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If you are going to make changes to the substrate (you mentioned sand for the Cories) there is no need to be gradual about it. Go ahead and make the changes now, before you add the fish.

Good to work around with the hardscape and get it where you want it.
It is OK to drain the tank to work with the lay out, try different things.
When you think you have a nice lay out take a few pictures. If you decide you like that one it is easy to re-make it from pictures.
The bacteria do not live in the water, but on all the surfaces. As long as you refill it and turn the filter back on at the end of a session they will be fine. Put the moss ball into a bucket of water while the tank is drained.
Continue feeding the bacteria daily while you are working on these details. Then, when the right fish deal comes along your tank will be biologically ready.
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