It'd be a 30gallon with sand substrate pushed up in a mound and then tapering out to give a section of water and land (50/50 land water) the problem is i'm not sure how to filter it. I have an external fluval 205 on that tank now but i don't think that it would be able to suck up the water well because it is a gravity fed siphon (that's how they work) and i'm not sure it would be able to suck very well if the water level was so low. So how are these tanks generally filtered.

Hi
It would be possible to use your external filter as long as you keep water levels a few inches above the water intake pipe of the filter. Use Mangrove plants as an added natural filtration. Use a deep sand bed as your main filtration.

Experience.

Hi. Any simple underwater filter can be used, an air-powered sponge filter, an internal power head type canister filter, even a low flow pond filter. Just be mind-full of the suction and return flow, they can't be too strong. pets question and answers,www.5d2d.com
You also have to watch any cords you put into the tank as mud skippers will climb and escape, a good fitting lid is needed but ventilation is also very important.

Rather than add more here for you, try this site it's a good read about mud skippers.
http://homepage.mac.com/nmonks/Projects/…

Past experience and reasurch