i think you need to be able to build and delete a lot of towers right now, which means having the sprouts/minerals/ingots to do so.
so build, time boost, delete (about what… 50 times?)
then build, time boost, upgrade time time boost, delete.
then you might have the total number of dark matter needed to complete all portal upgrades.
that's ignoring quests that require you to have 10 towers and 10 breeding facilities at the same time, or assuming you do all of this after that point.
personally i would go to the point of having the 10 and 10 for the quest, and then maybe use 5 towers on a build/delete/produce rotation to supplement your magic supply and make the dark matter. at least that way you'd get a feel for how much you're using before you build yourself into a corner with no options.