I cannot figure out how to load fuel into the second tank of the fusion reactor in NC 2.2. No matter how I place the fluid pipes, only the first tank is filled.

I was trying to use Helium straight from the helium accumulator. So no, my problem is that I was trying to use a fluid that was not a valid fusion reactor fuel.

Ah, ok :)

Are you using the same fuel in each tank, or two different fuels?

I tried different fuels after I couldn't get the same type of fuel into the tank. No fuel can be loaded into the second fusion reactor tank, regardless of how I place the pipes.

I can't recreate this issue - are you on a server?

No. Now that I think about it, I tried to fill the reactor with mekanism hydrogen- I'll do some testing and see if it works better with fuels from nuclearcraft.
UPDATE: I think I know what went wrong. I was using an electrolyzer to fill the first tank, so even though it looked full on the ui, it wasn't full yet (and it was filling really slowly). Meanwhile, the other fuel that I tried was helium, which doesn't seem to work in the reactor.
I suppose that this begs the question though: how do I get the non-hydrogen nuclear fuels? I can't put helium in the neutron irradiator to get helium-3, as far as I can tell.

Helium (i.e. Helium-4) is not a legitimate fusion fuel - Helium-3 is, however. The electrolyser produces hydrogen, deuterium, tritium and oxygen. All of them but oxygen are legitimate fusion fuels, but the deuterium and tritium production rates are very low. What might have been happening is that a small bit of deuterium or tritium was clogging up the second tank.

The possible fuels are hydrogen, deuterium, tritium, helium-3, lithium-6, lithium-7 and boron-11. You can get the first three from the Electrolyser, but can produce more deuterium and tritium as the products of fusion reactions (although there is a small issue as explained at the very bottom). Helium-3 is produced solely through fusion reactions, and lithium-6, lithium-7 and boron-11 (and boron-10) will be produced by melting down the corresponding isotope items in the Metal Melter, but I have not yet added the recipes for said items (I will do soon). All of the fusion reaction products correspond directly to the real-life products of such reactions.

The Neutron Irradiator is another way to produce more tritium by bombarding lithium-6 or boron-10 with neutrons. Each reaction produces tritium and helium-4, but as boron-10 is heavier, it produces more. A legitimate real-life reaction can be achieved by bombarding lithium-7 with neutrons, but this reaction is not in the mod as neutrons are also produced, which would make producing tritium too easy - you could just cycle the neutrons round.

Helium-4 can't be formed from helium-3 and a neutron, as helium-4 is far too stable (one of the reasons it's such a common product of fusion reactions). Instead, the helium-3 and neutron would react to form tritium and hydrogen, but it seems I forgot to add that recipe, so bear with me :P

I was just experimenting with the fusion reactor, and for some reason, some of the products for particular combos are a little messed up (the ones where the same fuel is used for both inputs), so that's another thing I need to work on. For example, the hydrogen-hydrogen reaction should produce only deuterium, but for some reason it's producing helium-3 and neutrons...

So yes, the mod still has some issues here and there, but it's to be expected when attempting to add content so rapidly - what is for sure is that JEI integration is beyond crucial now :)