Upkeep is the amount of money that is taken away from your hourly income. When you buy henchmen and vehicles, you will see a value for upkeep. For example, if you were making $10,000 an hour and you bought a Vehicle with an Upkeep of $1,000, your hourly income would be $9,000.
Henchmen and vehicles make your attack/defense scores higher, increasing your chances of winning against your opponents, but also lower the amount of money you generate.
Try to keep your upkeep at about 20-25% while arming up all of your alliance members with the strongest available henchmen and vehicles at your level.