Use your factory via the Factory tab in your menu once you've finished the hacker mission on Zerard. The factory thing can be a bit confusing, but it's not really hard once you figure it out. The first plan you receive is for the Magic Smelter. I'll use it as an example to roughly tell you how it works.
From the Factory menu, go in and choose the plan then say yes when asked if you want to use a template. The factory will then drop in the best starting set-up for your product. The smelter has two ingredients, which should be placed on the two source tables at the top of the screen in the same order listed in the plan. If you look in the user manual in the Factory menu, it will tell you what each type of material requires to break it down. Always remember that ingredients must be broken down to be used, and each type of ingredient is broken down in a different way. One of your ingredients is mechanical, which will require a disassembler; the other is a circuit, which will require a washer. Basically, you have to break down all of your ingredients into forms the smelter can use, so each ingredient has to go through its respective piece of equipment to work. So, remove a couple tubes on the line for the circuit and add a washer; on the other line, aremove a couple tubes and add a disassembler. You will need to add a couple curvy tubes (rotate as needed) to then hook the disassembler into the line.
Next, you have to make each ingredient hit the assembler (that big piece near the end) at the same time. Each piece the ingredients go through is numbered, and everything was equal until we added the washer and disassembler. The washer takes a count of two for the ingredients to pass through; the disassembler takes a count of four plus a couple for the pieces to hook it into the line, so the left line is running four counts faster than the right. See what I mean? So, you need to add four more counts to that line. It's easiest to move your source table and add extra tubes on that side. I'm doing this from memory, so I may not be remembering the numbers exactly, but you should be able to get the concept.
Finally, go to Place and choose Power Cords to plug everything in. Run the cords from one of the hooks on the side to the plugs you can see on the two source tables, the washer, the disassembler, the assembler, and the completion table. It should make an electrical buzzing noise when properly plugged in, and pieces that move will start to do so. If you're ever having trouble with a cord (just for future reference), you can run a cord and hit X to set it then bend and go another direction. That's helpful when the cords don't line up the way you want.
Now choose Run (the last choice in the menu) and you should have a Magic Smelter and a trophy. If you get an error message, one of the steps has been done incorrectly, so you'll need to find the mistake and fix it then try Run again.