I wouldn't have two middle names for my child, no matter what the situation. It's just really not my style. I would probably have the child's father's name be the mn and call it a day.
Having two middle names is not confusing (as a former teacher and person with a large family, I can tell you from experience that it takes more than two middle names to "confuse" a child!) or even all that unusual; so I would say that if there is a middle name that you really WANT to use, especially if it is a family name or something along those lines (name of a dear friend, etc.), go ahead. But if you are choosing another middle name just to choose one, I would say not to bother.
Ditto all this--our son has two middle names, but they were names we really wanted to use (and DH and his brother have two--it was something I wanted to carry on.) If you just feel like you should stick one in there, I wouldn't. Dad's surname will serve quite nicely.
Just wanted to comment on that also- I dont' think that two middle names are confusing, but do agree that if OP is choosing another mn just to choose one, I wouldn't bother. :)
I agree that two middle names is fine if you really want to use another middle name along with the father's surname. It's not even something that you would necessarily have to carry on with all your children, if your situation happened to change later. My DH is the oldest of 3 boys. Only the youngest has 2 middle names. The first middle name is his dad's first name, the second middle name is his dad's middle name (and also his grandfather's first name). I think that it's nice since he was going to be the last baby. All of the boys were named after family, first and middle names.
Having 2 mns is very common in England, we all do, it's no problem at all, it actually makes it easier to keep your records distinct.