Unfortunately, it is going to mess things up.
If your son is not paying Fair Market Rent, then many of the deductible expenses would be limited to the space that is EXCLUSIVELY to the paying tenants.
For example, let's say that four bedrooms are each 10% of the space (40% total) and the 'shared' space is 60% of the house. In that scenario, you would be limited to only using 30% of most of the deductible expenses (the three bedrooms your son does not use).
You may be able to use 75% for some expenses that would be used on a 'usage' basis. For example, it would be logical to allocate 75% of the water/sewer bill to the tenants. But things like mortgage interest, real estate tax and insurance would be limited to the amount used exclusively for rental (30% in my example).
