I'm pretty dumb and this game took me forever to figure out, here's some of the things that I think need explained better:
1. To complete quests you need to put the resources into the hub, you do this with the Vortex gun thing on the left side of the hub.
2. You do not need the furnace to make ingots (obvious since you have to have ingots to craft the furnace), just select the recipe in your inventory and use the workbench/pad thing attached to the front of the hub. You have to shoot it with the vortex gun to craft it.
3. To set up the furnace or the big ass tower crafter to craft you need to select the recipe you want to craft from your inventory, then use the configure mode of the build/delete/config gun (located on your right hip) on the furnace/etc. This assigns the recipe to the furnace/etc.
4. The Build part of the build gun is for conveyor belts. Just select the output/input of a machine/hub and direct it where you need it to go.
5. Full automation is locked behind the moonrain ingot quest (I think the order was roughly iron -> gears -> copper -> wire -> circuit board -> moonrain so it's not that far into the game) , the reward of which is what allows for auto capture of the cubes, until then you will be manually chasing down cubes.
6. Once you have unlocked the Room/Shower/Dungeon Module you can access it by going through the portal and taking the elevator.
I'm sure there is more that I cannot remember as it has been a bit since I played. I also didn't even come close to finishing it. This is an interesting project that I hope gets some more gameplay tweaks as it is a bit rough at the moment, but still fun nonetheless.