Gravel can be kind of sharp for them. I used to use Aragonite and sand as their substrate. In the wild they bury in mud so softer is better for them. Anyway, hope this helps and good luck!
Here is a great place to get "LIVESAND"
If I was going to setup a tank for mudskippers I would first put a layer of Mineral Mud mixed with some Onyx Substrate, then I would mix some Marine BioSediment with LIVESAND. The majority of the substraight would be livesand.
I would then be able to plant mangroves and there would be a whole ecology setup already for fish to be added.
**Livesand is for saltwater.
You can lower the salinity slowly to high-brackish I wouldn't go below 1.012.