I've posted this a few times over the years, so here it is again:
The main concern people have about sand would be anaerobic bacteria build-up. Anaerobic meaning without air, though more accurately, without oxygen. If you didn't know, the ammonia and nitrite reducing bacteria require oxygen to work (to convert ammonia to nitrite and to convert nitrite to nitrate).
Anywho, under anaerobic conditions, bacteria start to get their energy from other sources, like reducing sulfur instead of oxygen. And a by-product of that is hydrogen sulfide, yes, one of the deadliest compounds in nature.
But, there is relief. In water, as soon as hydrogen sulfide comes into contact with any oxygen, it will become harmless. So, even if there is a pocket, and even if you accidentally stir it up, it will become harmless as soon as it hits your well-oxygenated water. And you know your water is well-oxygenated since your fish are living in it, and they need oxygen. This is the stinky smell you got, sulfurs, but you most likely smelled sulfur oxides, not hydrogen sulfide. Like I said, hydrogen sulfide decomposes very quickly in the presence of oxygen while in aqueous solution.
So, there really isn't anything down there to worry about, so my recommendation is to not stir it at all. Just vacuum the top of the sand to get the uneaten food off the top. If uneaten food on the top is a constant problem, you probably should be feeding less, maybe a lot less. If it really bothers you, maybe decrease the thickness of your sand layer.
p.s. Another source of energy anaerobic bacteria may use is actually to convert nitrates to nitrogen gas. This is what living rock and living sand does for some marine tank setups.
Here is another quote from another post of mine:
Diana Walstad in her book Ecology of the Planted Aquarium actually talks about the beneficial aspects of having anaerobic conditions under the substrate near the plant roots. She has around several inches of soil as the substrates in her tanks. The anaerobic bacteria will use most anything for an energy source, reducing nitrates is just one of them. The bacteria can also reduce iron, sulfur, manganese, and so on. The great thing for plants is that these reduced forms are much more easily taken up, so anaerobic conditions help the plants get their micronutrients.
