You'll need to investigate and do some tracing. The 2 pipes (hoses?) coming out of the portable are likely the waste/pumpout hose and the vent hose. Pumpout hose would be over 1" in diameter, the vent hose about half that. Is that what you have?
The 'waste' tank that you see in the boat might be a 'grey water' holding tank plumbed to the sink in the galley and/or head. Those are becoming common as states increasingly limit what can be dumped overboard. You should have a second tank that holds fresh water to feed the faucet(s).
Based on my experience, it's unusual for a modern 24-25' express cruiser to have a full marine head with waste tank. They're more likely to have either a portable toilet with removable holding tank, or a similar unit plumbed so that you need to use a pumpout station to empty it (called an MSD). I think you have the latter. My '99 Chris Craft 240 was plumbed as I think yours is and I hated it with a passion. A lousy 2.6 gallon waste capacity and I needed to go to a pumpout station to empty it. Whoever thought up that scenario shoulda been shot.
My .02
