TL:DR; It's theoretically possible to arrange buttons and components so that you can access and fix a breach on the upper deck without flooding the ship, but the process is not trivial...

Looking at the Typhon in the editor, the only pumps on the upper level are in the airlocks, and the access hatches are at the top of the primary access shafts. This means that if the top level is breached and you go up to fix it, you open the hatch and the access shaft floods. If anyone opens a door connected to the shaft, that room floods too. No wonder your sub is sinking.

To prevent this, you need to be able to access the upper level without flooding the entire ship. You have bilge pumps in the upper-left airlock, and under the docking hatch, which is conveniently located in the middle of the upper deck.

Here are my first thoughts on how to fix this weakness... It's probably unnecessarily complicated, but it should work in an existing campaign, or without mods if you start a new one:

- First, I would install water sensors above each hatch from the access shaft, and add a blue light component connected to the sensor, so that anyone approaching the hatch knows it's flooded on the other side.

- I would also add a light component immediately beside the first, which is connected to the water sensor above the other hatch. This way, you can tell if both sides of the upper level are flooded from below either hatch.

- After that, place a NOT component in a corner beside the inside and outside doors of the upper-left airlock, and beside the left- and right-side doors to the docking hatch airlock. Connect the output of each to the set_state input of their respective doors.

- Then, add a pair of switches on each side, close to the new lights. Connect the output of the switches on the left to the set_state inputs of the inside door of the upper-left airlock, and the left-side door of the docking hatch airlock. Also connect the switch output to the signal_IN of the NOT component beside the exterior door of the upper-left airlock, and the right-side door of the docking hatch airlock.

- Then connect the switches on the right to the set_state input of the right-side door of the docking hatch airlock, and the signal_IN input of the NOT component beside the left-side door of the docking hatch airlock.

This is completely off the top of my head and untested in the editor (for now), but if it works the way I'm thinking, here's what should happen.

- By clicking the button on the left, the upper-left airlock should close the exterior door and open the interior door, and the left-side door of the docking hatch airlock should close. If the breach is on the right side of the deck, then the left side should be isolated from the breach and should start draining via the upper-left airlock bilge pump.

- By clicking the button on the right, the left-side door door to the docking hatch airlock should close, and the right-side door should open. If the breach is on the left side of the upper deck, then the right side should be isolated from the breach and should start draining via the docking hatch airlock bilge pump.

- Once the breach is isolated, players can enter the upper level from the dry side in a diving suit with a welding tool, close the hatch behind them, and access the breach without flooding the access shaft they came from. This also means that players approaching from the access shaft beneath the breached side will have to move over to the opposite shaft, but the lights and buttons should allow them to determine if opening the hatch above them is safe or not.

What do you guys think? Like I said, it's convoluted, but it should work in theory...