Claiming her wages in your flexible spending account is a question for the plan administrator. Each plan is different and they would know the rules.
If it is allowable, you will need to file quarterly payroll tax forms (941, 940, & state unemployment). This is where you will withhold federal taxes, state taxes (if any), and soc sec & medicare.
Hope this helps.
If you have any other questions, you can get my e-mail from Jack.