Generally, MegaTowers are difficult to balance to make a profit from, so it might be wise to leave them off for the time being.
Omega costs money for the materials if you can't mine them obviously, in return for hourly profits. Maybe you need more industrial/commercial to collect more omega profits. Another thing you can try is adding some drone producers to make more money. Processors might seem expensive but even a full line of drone makers takes a long time to use them up.