The U.S. petitioner pays the USCIS filing fees, but how the group allocates that cost internally is an accounting and tax matter. Keep the allocation consistent with the statement that the U.S. entity controls the employment.
Let the cost follow the entity that employs the engineer
The Form I-129 base fee, fraud-prevention fee and any premium-processing or asylum-program fee are listed in the USCIS fee schedule and are paid by the petitioning U.S. entity. Which company ultimately bears the cost in the group's books is a decision for the group's accountants, subject to transfer-pricing and tax rules on both sides of the border. There is one immigration consideration: the petition asserts that the U.S. subsidiary will employ, pay and control the engineer while he commissions the New England line. An arrangement where the Canadian parent continues to pay him and merely lends him to the subsidiary can still work under the L rules, but it must be described accurately, because the offsite-placement limits turn on who controls the work. Professional fees for preparing the petition and organizing the technical evidence are usually the larger cost and should be budgeted separately. Confirm fee amounts on the schedule at filing.
Hypothetical example: a packaging-automation company must decide whether to file promptly for a vision-systems engineer or first finish technical exhibits. The fee schedule establishes the filing cost, but dated manuals, project logs, and the U.S. scope establish the case. Budget professional preparation as a separate decision from government fees. Spending on an expedited adjudication does not cure a thin specialized-knowledge record, so the company should finish the evidence sequence before choosing a processing option.