Also be aware: I encountered a bug when building the second factory. As far as armory upgrades go, it considers the level of your SECOND factory for meeting prerequisites to upgrade units. So despite having a level 4 factory, you are no longer able to upgrade anything until your second factory is sufficient level to open up the upgrade in question.
Currently the CS solution to this is to remove your second factory, as they did this to me. But then I was out the 30k oil and 4 citizens for 4 days with nothing to show for it, so I received a crown reimbursement for the time and rss. Apparently they are aware of the issue and are working with players (at least they did with me).