The mulm in a planted tank supplies the plants with food. I don't keep puffers, so if they are particularly messy to where you have stuff building up, you can siphon just above the surface with a small bore siphon to pick up the loose stuff.
Here's a thread with pics of my Onyx tank. I might siphon clean it some as described every few months. Or not. The snails and plants process pretty much everything. (With puffers, you don't have snails