Very confusing at least to me. So you make a light tower. Level it to dark. Not sure where that blue circle thing is made. Assume breeder. Sell it and rinse repeat 72x?
The object is to produce 72 black matter. To make 1 black matter requires 2 light towers and 1 dark one.
This is an example of how to get 1 black matter.
1) Start the build of a light tower
2) Sell it immediately to get 1 white matter. You don't need to let the build complete, but you can.
3) Start a 2nd light tower, let the build complete.
4) Upgrade it to a dark tower. One of the goods required is that white matter from the sold light tower.
5) Sell it immediately and you get 1 black matter.
If you don't sell the light tower, it starts producing white magic, the light-colored bottle. It does this like a house producing coins. No input is required. Similarly, dark towers produce black magic, the blue bottle. The white and black magic are the capped goods, which can be gotten via PPs., if you have enough (no, I can't define 'enough'). Thus, you don't need to produce the magic, so don't need to keep the towers around. However, as I mentioned above, they are needed for a couple of storyline quest.
When I started the chapter I build a good number of white towers, selling half and letting the other half be upgraded to dark ones, replacing them as soon as I could to get that needed black matter. You need 24 black matter to build the portal and 24 for more for the 1st two upgrades. Hence, 72 total. That is the only purpose for the black matter.