Not silly at all.
You first need to have your r/o water or your conditioned water from the tap the same temperature as your tank. If you are using tap water you need to let it set overnight as well as follow the manufacturers directions on any type of product you add to it.
A python siphon is the best bet to get down into your gravel and remove and wastes, if you don't have one you can pick one up at your LFS. Most owners are more than happy to give you a run down on how to use one.
You then drain your percentage of water out of your tank after you have cleaned your gravel and replace the water removed with the new water. You can clean any decor as needed during this time. Remember not to use any chemicals or soaps on decor, but a rag and some warm water usually gets any algae right off.
Water changes are kinda difficult once you start. It gets much much easier the more you do it!
Someone should make a training video and put it on youtube or something...
My Puffers: Puffers I have kept: T lineatus T miurus A modestus T biocellatus C valentini C coranata C papuan C lorteti DPs suvattii burrfish T niphobles
What kind of substrate? Just drain out 1/2 the water, add 1 drop Prime/gal (a dropperfull treats about 20g) & then fill with the same temp water from the tap. Don't worry about adding salt for now.
You are getting sleepy... you only hear the sound of my voice... you must do water changes... water changes... water changes... water changes...