Do you want to destroy some of your old factories because there isn't enough room? You probably do, but in the beginning of the game it said not to! If you press G then go to Stored then you can see how much of a certain shape is stored in the Hub, use this page to see if you have got enough of a shape to delete the factory.
This can be adapted into a strategy which will reduce the messiness of your factory. This simple yet boring method consists of starting be collecting nothing but uncoloured circles until you have 1825 of them, you will then delete all of your buildings and belts and begin collecting the next shape for however many you need. This strategy is extremely slow and after a couple of hours you may have only reached level 5 but it is good if your factories get very crowded and even laggy because you are only producing one shape at a time. Consider trying it out!
The shapes are in order required for leveling, then the upgrade-only shapes at the end. The blueprint shape is at the very end, since unless you're doing the previously described strategy, you will need it infinitely (and even with the strategy).