It complicates it. The affiliate is the petitioner and must show it can pay a senior salary; a manager paid entirely from Canada while working full time in the U.S. raises questions about the genuineness of the U.S. role and creates tax issues. Structure U.S. payroll and let the parent reimburse if needed.
The petitioner should look like the employer
USCIS fees on Form G-1055 for Form I-129 are paid by the petitioner, and premium processing is optional. Those amounts are minor beside the salary question. The petition asserts that the affiliate will employ her in a senior managerial role, and the natural evidence of that is a U.S.
payroll record, benefits enrolment and tax withholding. An arrangement where she remains a Canadian employee seconded at no cost to the affiliate can still be an L-1A, since the statute allows the foreign employer to continue paying, but it invites questions about whether the affiliate genuinely controls a manager it does not pay, and it creates cross-border tax and social-security issues for her and for both companies that the immigration file does not resolve. The cleaner structure is U.S.
employment at a salary the affiliate's revenue supports, with an intercompany agreement if the parent wishes to fund part of it. Get payroll tax advice on both sides before the petition is drafted, not after admission.