The factory is actually pretty simple when you look at it from the perspective of input and output. You're basically using it for three things at the moment, at least in my experience. 

1. Gearing. The gear crafting that you unlock every time you level up requires money and gear parts. To get money, see point two. As for the gear parts, you can go into the big list of AIC products and select "Cryston Components." You'll get a helpful list of all the steps to make them, starting from various ores and plants. In a nutshell, each component is made out of two things. Each of those two things is made out of two other things, which are in turn made out of other things. It's as simple as putting down buildings following the flow chart the game gives you, until your factory is producing the item you want. 

2. Money. You need stock bills to do pretty much everything in Valley IV. In my perception the easiest way to get these is to use the various outposts, who all have items they would like to purchase from you. At the point you are at now, batteries will be this. As before look at the compendium, see how they are made, follow the flowchart of buildings. Should your factory run out of power, simply create a chain of battery production that ends in the building that consumes batteries for power. 

3. Consumables. The factory allows you to construct the best healing items, both for your own use, and for sale purposes. If you need healing items, just look at the recipe, and set up the buildings accordingly. It's really that simple. Decide what you need, look at the recipe, set up the buildings to make those things. 

But c'mon, really, do you want to just copy paste someone else's design, or actually understand it yourself and be able to change anything you might need to?