I put substrate then rocks, pots, ornaments then pour the water on to the rocks as not to disturb the substrate because i use sand, or you can put a plate in to pour the water on to and remove the plat and lastly plants.
I do substrate and then Water about 1/3 full. Then hardscaping and maybe a couple plants. Then another 1/3 water (2/3 full). Then finalize all the plants. Rearrange everything how I want. Then I fill completely.
I put the substrate in, then water (using a plate to stop disturbance of sand) & then the hardscape & plants. (Aside from my saltwater aquarium where I put the live rock in before the sand to ensure the live rock wouldn't fall when stacked.)