Although not explicitly stated, it seems clear that Jojo was acting on Charlie's orders during the Portal Run of Book 2, by delivering the Dismiss Perfect Warlord scroll and arguing in favor of letting Parson through Jetstone's portal.
Jojo has told Parson that he considers Charlie to be his benefactor. Precisely what Charlie has done for Jojo is not yet known. It may involve training as a Carnymancer, revenge for the fall of Unaroyal, or assistance in the difficult task of simply surviving as a barbarian carnymancer. In any case, Jojo has apparently done business with Charlie before and signed a non-disclosure agreement.
Roger Victor Clarence believes that Jojo's true loyalties are to Royalty and that his work for Charlie is a ruse. Jojo claims to be willing to work with Roger to take down Gobwin Knob and Charlescomm both so as to transfer their Arkentools to Royal ownership.