Oxygen not polluted

I've been playing a lot of Oxygen Not Included lately. (That is: "A lot of" by share of video game time this week. In absolute terms only about four to five hours.)

It is a complicated game. There are a lot of specific items you can build, mine, research, etc. in the early game. I've completed all basic research options and at this point I have 12 menus each having on average about 5 to 6 choices. This includes:

1. Walls/floors/ceilings ("tile") and doors. Ladders. Storage boxes. The good stuff.
2. More specific base stuff. Manual airlocks. Walls/floors that are permeable to one of liquid (mesh tile) or gas (airflow tile).
3. Five different buildings for producing oxygen. Oxygen from lots of algae. Polluted oxygen from polluted dirt. Algae to remove CO2 and add oxygen. Water into oxygen and hydrogen. Rust into oxygen and chlorine.
4. Power generation, storage, wires, and a switch. Three generators (manual, coal, and wood burning) and two battery options.
5. Food. Food paste maker, electric grill, two ways of planting crops, a ration box and an egg cracker.
6. Plumbing. Big one. Includes outhouse, lavatory and shower, but not wash basin or sink. Manual pump and bottle emptier, liquid pipes, pump, pipe vent, filter, and valve for limiting flow.
7. Ventillation. Similar options to plumbing but no bathroom stuff and no manual pump/filler. There is a semi-automatic filler, I think.
8. Refinement. Four options that are not much like each other except that they turn stuff into better stuff. Compost, rock crusher, kiln, and sludge press.
9. Medicine. Lots of stuff! Wash basins and sinks, hand sanitizer, apothecary, sick bay, triage cot, massage table, tasteful memorial.
10. Furniture. Lots of fancy decor. Also: Water cooler for people to meet at. Table to eat at. Beds. Lights.
11. Stations. Like refinement if slightly more coherently techy. Research station and supercomputer (which is also only for research, but for better research), skill scrubber, crafting station, and oxygen checkpoint plus mask dock.
12. Automation. I have no refined metal, so I can't build any of this, but if I could, I'd have automation wires, a signal switch, and a duplicant motion sensor.
13. Rocketry. Just a telescope for now.

That is a lot of options to remember I have. Most do not seem important right now. Who needs medicine when you're only mostly able to feed your colonists and some are balanced on the morale tipping point between contentment and stress? What do you need rocketry or a supercomputer for if you are still using outhouses? Why build an egg cracker when you are still powering your base with a hamster wheel ("manual generator") and a couple leaky batteries?

This isn't the tricky part though. The tricky parts at the moment are:

1. There's this polluted water scattered all over my base and it's emitting polluted oxygen. I have a dump bottle emptier set up for polluted water; why isn't that stuff getting dumped?
2. I'm getting slimelung germs from the marsh biome where I'm dumping my polluted water. Can I get rid of those germs? They're leaking into my base a little. Also, is 2,000 a lot of germs? Some marsh blocks have as many as 800,000. So I guess not? It's probably fine?
3. I definitely don't have enough labor to keep up with all the things I could be building right now. But also if I printed them then I wouldn't have enough food and bathrooms to feed them.
4. I'm not sure how to keep track of my duplicants (dupes) and what they're up to or getting sidetracked by? There's following but that seems a bit inefficient. I can find each individual one by clicking on them in the Vitals menu but I'd really like to be able to see at a glance, "Nikola is washing his hands, while Camille is supplying construction material." I'd like to be able to debug why my dupes are
5. Maybe polluted dirt and slime inside a bin still expels polluted oxygen? Dang, that's inconvenient. Hmm, but wait, when I hover over the slime in the contents it doesn't say it's emitting anything, and when I click on it it says emitting 0 kg/s. But I'm still seeing these nasty yellow bubbles. Is that germ emission? But the contents panel also doesn't mention slimelung germs, even though the surroudning oxygen has 137 of them.
6. Also I have egg shells inside that bin?! And wow there are a bunch of food poisoning germs on the stuff in that bin. Like 1.2 million of them. Maybe that's why I'm getting food poisoning.
7. I am running out of water (about 1/3 of my current reservoir). I have a few other pools, but they aren't as convenient to tap. Unclear if I should worry about that.
8. I'm getting a warning about insufficient breathable oxygen but the breathability overlay looks mostly fine. There's a bit of red from CO2 but most of it is at the bottom of my base or the pumps. The upper levels are all breathable or very breathable.
9. Not sure what to do with all this CO2? I probably should have built my coal generator at the bottom of my base to avoid this unbreathable gas settling down into the pits in my base. But I didn't realize that's where the CO2 would want to go. There's nowhere convenient nearby to dump it. There's these plants but they only consume 0.3g/s? So I'd need around 66 or 70 algae terrariums to balance out one coal plant. That means digging out 140 tiles of space which is A Lot for one building. That is clearly too much. Maybe I can just ignore it? Or I could build a smaller number and hope the coal generator doesn't run often enough to outpace them. At 600W = 0.6 kW it should take (50 kJ)/(0.6 kW) = 83.3 seconds to fill up my batteries. My base is using 538W right now which seems about usual. So – it looks like it may average out to the same as running constantly. So I can't get away with much less. Maybe I should have built my coal generator at the bottom of my base? Mmm.
10. The disinfect tool only seems to work on buildings?
11. I built my rooms slightly too tall (4 tiles high of empty space, or 6 tiles including floor and ceiling) and now my dupes can't reach the ceilings in some places to fill in the last few tiles. To add/remove wires or decorations, which is a little annoying.
12. Should I even bother with a refrigerator yet? Some of my food is rotting in the ration box but 120W is a lot right now...
13. Whoops, I put lights over my beds for decor reasons, apparently that bothers dupes. Imagine. Well I guess I should remove those.
14. I guess I should care about decor. I've got wires running through the middle of rooms and I've got debris everywhere and the dupes don't like it. But construction takes so long...

There is more but I'm going to ignore it for now because this is already too long.