Or you could do it all at once, if you can handle the risk of mini-cycle (daily partial water changes) if something goes wrong.
I replaced all the substrate in a gravel tank I upgraded to Eco-Complete. I took an eight gallon bucket (aquarium use only) filled it with water from the tank, removed all the plants, then removed all fishies and inverts and everyone into the bucket. I took no precautions as for loosing bacteria in the gravel since I have a lot of biological filtration in place (1
HOB: AquaClear 70 with extra sponge + 1 Wet/Dry
sump: Pro Clear Aquatic Systems model 75) for this particular 40gal tank.
I disconnected power from everything except the lights. I emptied the whole tank (keep in mind I had a bucket with 8 gallon with airstone + around 10gals in the sump). Removed the gravel with a beach toy shovel (courtesy of my daughter Camila), dumped in the new substrate, added treated tap water, waited for 30 minutes for settling, turned everything on. Once temp was in range, I replanted the whole thing and introduced fish back in. I did monitored water parameters for a couple of days, everything went OK.
I guess if you take a nylon stocking and introduce a good bunch of gravel from your tank and hide it somewhere (if not don't bother too much, in two weeks you'll take it out anyways), you could replace all the substrate at once.
I took me three weeks of planning ahead so filter media was unclogged and undisturbed for the previous two weeks. I still made mistakes (e.g. had to add 1/2 bag of substrate later on repeating the whole process).
If you want your plants to thrive in low light, I recommend using Eco-Complete instead of sand. Swords would die on my tanks that now have Eco-Complete; Anubias, already slow growers, are as good as it gets in low tech tanks.
I took an extra step and added
DIY CO2 (yeast+sugar recipe), still checking things out. Also added 9W extra just on top of the light demanding Amazon Black Swords (with a compact fluorescent light).
Eco-Complete may look expensive, but is definitely worth it.
Pepe
Santo Domingo