I have a 2001 Nitro 175 Sport F & S. I am sure they are quite similar.
The ski compartment does not have a drain. It also does not have a watertight seal around the deck lid. If it gets heavy rain or water from boarding swimmers/skiers the water will pool in the compartment. 3 - 4 inches of water seems alot as it is somewhat a large compartment. If you are sure it is not from rain, melting snow or boarding swimmers/skiers, then try this. Make sure all water is out of bilge and livewell and wherever else it can get; then put water into the compartment and watch where it drains to. If it comes in, it also has to go out. You'll find your source. The boat needs to be on the trailer to check this. My guess is it comes from some source I mentioned as it is not directly open to other sources.
As to the two switches, my boat does not have them but, I'd also think they are p & s fuel tanks.
I don'tknow of any existing plumbing schematic.