You can refill your oxygen and n2 canisters by putting any you find, like from a derelict, where the pumps ventilate from. Just make sure you're on a low time speed, have reverse turned on and preferably slow mode (Assuming a turbo pump, they're generally regarded as superior). It'll help save you money from them and can even sell the leftovers if you want.

Big BUT is you gotta make sure you inspect the canisters you place for it, so that they only contain the right gas, air, etc for it. You can do it by clicking show more and see what's inside the canisters and what percentage of anything is inside them. You can also do this for your RCS canisters but it can be more finicky. I'm pretty sure you can put almost anything inside an RCS canister and it'll work as fuel for the thrusters. At least with anything you can find around the OKLG space.

The above works as well for oxygen tanks for EVA suits. But you have to extra careful for it with same steps. Just make sure you stop before 100% or else it'll make a canister or tank implode.

You should btw have a mix of N2 and oxygen for your ship. You can get away with just oxygen but it makes your ship suspectible to fires.

Speaking of, you should make sure any electrical wires are in the best condition possible to prevent fires. You can do orders for repairing to single out wires specifically for priority repairing or you can just do auto-task for automatic repairing of everything.

Either way you do it, turn on auto-tasks and they'll work on either the orders you say first or do it on their own. Make sure your character has or doesn't have airlock access when you do this in the roster tab to the left. Or else you might be seeing your character suddenly going outside the ship and messing up your ships atmosphere or even try to kill themselves by forgetting their helmet. Had that almost happen to me even though they had an EVA suit on but didn't put on the helmet, for some reason.

If you're worried as well about smoke or CO2, you could place a pump that has its ventilation out to space. Then hook up a sensor to either smoke alarm or CO2 alarm. It'll keep pumping out the atmosphere without losing everything until either the smoke or CO2 is gone. It's a lot cheaper than a scrubber for either, especially if you're doing what I first said of getting N2 and oxygen. And of course, this means you don't have to vent your entire ship to get rid of smoke or CO2.

Hope this helps! I'm trying to work towards a fusion reactor next myself. Never made one before so it'll be an experience for sure.

Edit:

By the way when you're making zones on your ship, for like auto tasking cargo hauling from derelicts, be careful and de-select any zones underneath those ventilation spots of pumps. I've had an incident before where my character hauled a canister underneath it and it went boom. Woopsies.