They have already been married for more than 2 months but did not file anything thus far? He could have potentially already had an employment authorization document if they filed all the paperwork in a timely manner.
The fees are not going to be waived and they will have to submit all the USCIS filing fees along with the applications. In fact, your daughter will need to show that she is deriving a sufficient income to support her husband. If she is unable to do so, she will need to have a joint sponsor complete an affidavit of support on behalf of her husband and file that along with the rest of the petition. If he is a Canadian and entered the US lawfully, he will be eligible to apply for permanent residence on the basis of marriage to a US citizen and, along with that application, he will be eligible for employment authorization while the permanent residence petition is pending.
Please let me know if you have any additional questions or if I may be of further assistance to you in this matter