I did this personally myself.
I replaced my substrate with the fish in actually. I had neon tetra, peppered cory, and guppies. I had gravel and wanted eco complete so I could grow plants.
It's all about filtration. What i did personally is i cut back on some filter media to make room for new media. I didn't remove all of it, just some, like 25-30%.
I did a LARGE gravel vac 5 days and then 1 day prior to the substrate removal.
I turned off the filter and removed 50% water.
Removed the existing gravel. Added my eco complete slowly. I took my scoop and gently placed the new substrate it at the bottom. Took a while but hey, this is a major project.
Then once all the new substrate was in there, I added that 25-30% NEW filter floss into the filter. The water will have TONS of material floating around. Fish waste I assume. Which i why i wanted some new filter floss in there.
I then added 25% water back into the aquarium and then removed 25% trying to suck up as much floating material as possible. Then I added 50% water back in. You will still have things floating but that is fine. Don't focus on that that will all settle or get sucked into the filter.
I then turned on the filter. 2 days later I did another large gravel vac to get all the settled crap out.
You are going to have a restricted filter flow for a couple of weeks. Allow the filter 2 weeks before you clean it, let the tank adjust and get used to the major change. Clean the filter properly (In a bucket of water from the tank) after the 2 weeks.
Then plan on changing out that filter media in 33% chunks. It will be very clogged up and you really need fresh media in there to get the flow going again. Obviously you dont want to replace all the media all at once or you will lose your cycle/BB.
I don't claim for this to be the proper way to do it, but its the way I did it, and I had success.
I didn't lose a single fish and neons are very fragile.
I hope this helps.