First, the FMLA permits you to charge FMLA leave concurrently with sick and even vacation time, if the reason the employee is absent is due to the serious health condition of a spouse, parent, child or the employee himself or herself. Thus, if you had wanted to, you could have informed the employee that the time away up until now "counted" against the 12 weeks of FMLA leave to which the employee is entitled.
Second, the interaction between the FMLA and the FLSA is somewhat complex and, therefore, the Wage and Hour Division has issued a specific regulation on this issue. It is found at Reg. § 825.206, which is on the Internet at
http://www.dol.gov/dol/esa/public/regs/cfr.../0825.0206.htm. It provides a special exception whereby pay can be docked for even partial days of absence due to FMLA. Be careful, however, as sometimes a state will have its own wage & hour laws which would be violated by use of this exception. It is best to consult with someone who is knowledgeable in this area of the law.
Finally, based on your description of the situation, it may turn into a situation in which the employee is gone much more frequently than 2-3 days per month. If this gets really bad, you may not be able to function with a replacement or other attempts to cover the absences. While it is an agressive approach, it is possible that you might be able to require the employee to be off continuously. Please email me if you would like to discuss this aspect further.