The U.S. affiliate is the petitioner and pays the USCIS filing fees. How the group allocates that cost is an accounting matter, but the allocation should be consistent with the affiliate being the real employer.
Let the petitioner pay, and let the books say so
Form I-129 is filed by the U.S. affiliate, and the base fee, fraud-prevention fee, any asylum-program fee and any premium-processing fee on the USCIS fee schedule are its costs. An owner who controls both companies can move money between them, but the petition asserts that the affiliate employs him, sets his salary and bears the cost of his role, and the accounting should match.
Paying the filing fees from the Paradise company's account, or having the Paradise company continue to pay his salary after the transfer, invites the question the petition is trying to answer. Professional fees for preparing the petition and organizing the evidence are the larger part of the budget for a small group and are also properly the affiliate's expense. Relocation, housing and travel are business decisions.
The owner should also budget for the Paradise company's cost of a manager to replace him, because the Canadian entity must keep operating for the relationship to survive. Confirm current fee amounts on the schedule before filing.