It can be hard to describe sounds, but I'll try.
A huff is a deep breath of air being forced out. This an exasperated sigh. The mouth is closed, and a huff simply seems to mean "please don't step on me/eat me". It's nothing to worry about, and even the tamest skinks can huff often.
A hiss is an open-mouth warning to stay back, and it sounds just like a snake. It's usually accompanied by that bright blue tongue flaring out. The skink is upset/scared and will probably bite if provoked. Let it calm down.
The noises to worry about sound moist. Think pneumonia in people. Or if you've had a wet cough, when you breath you can hear the moist noises. ST covered the descriptions: wheezing, crackly, popping, clicking, bubbly.
Normal breathing doesn't really make much noise. There can be a bit of a crackle if the skin is dry or the skink's going to shed, but it's not moist sounding.
Check for bubbles around the eyes/nose/mouth, in addition to the moist noises. And if you're worried, go visit a reptile vet (though any good vet would be okay if there isn't a reptile vet). If the skink is fine it barely costs anything for the vet to give a quick listen. And if there is an issue the vet should be able to treat it right away.
I agree with ST, avoid the splinter-substrates. I always found splinters got stuck in eyes/mouth and under the scales
I use shaved aspen usually (the big shaved bags found in many stores), or coco-bark (from garden centers) when I want more humidity. Coco-bark is more eco-friendly than cypress, otherwise I'd use that.
From what I've read online most people say its normal as long as he isn't wheezing or breathing hard. Problem is, I don't really know what those last two sound like. If anyone has a recording or video I'd appreciate it. I have him on Eco-earth that dried out a little so I assume its because it got a little dusty and he keeps burrowing in it. I've remoistened it all just to be sure and I'll definitely switch to aspen soon. Any good brand recommendations? I saw a big shaved bag in Walmart that looked nice and a lot of what pet stores carry are the splintered kind. Also, would cypress mulch be a good alternative since he is a Merauke. Thanks. 
Determining if a skink is breathing hard can be a challenge if you are new owner since they "huff" a lot, but wheezing will sound very wet, and can be accompanied by other symptoms like bubbles from nose or popping/clicking sounds. They sneeze, A LOT! 
