Planted Tank Guru
Join Date: Jan 2010
Location: Contra Costa CA
Most people do cap dirt. Sand or gravel works. If you look in the Substrate part of the forum you will find a lot of posts about this.
Disturbing dirt will often release ammonia and other things to the water column. If you had fertilizer tablets or Osmocote in there, or anything else that was supposed to be buried deeply and slow release, well, it is now fast release.
Better to plant when there is no water in the tank, just very wet substrate, and mist the plants.
Then, when all the mess is done, you can fill. Put a plastic bag or plate over the substrate and allow the water to run in slowly over the edge of the plate and seep into the substrate.
At this point:
I would do a water change, and use small tubing, perhaps air tubing, to vacuum the leaves and other surfaces with dirt. Or wave your hand near them to create enough water movement to dislodge the dirt. Do as big a water change as you can by digging a small hole in the substrate and pulling some water out from below. This should settle the dirt that was drifting in the water.
Monitor the parameters for several days for ammonia, and for a week for other ferts (if you used any) that might be somewhat slower releasing, but that could raise the GH, KH, TDS or other.
While you are waiting you can be doing the fishless cycle to feed the nitrifying bacteria.