I have two Flemmies and love them and the breed. Yeah, they're big, so keep that in mind. Now some folks I've seen use a extra large dog kennel. I've never gone that route but it's quite workable. I've used X-Pens and NIC cages and from personal experience I would suggest the X-Pen. It's easier, more manageable and workable to any space. In my experience NIC cages are a bit of work setting up, a bit trickier to clean and once you set it up you have to tear it down if you want to do a different space design, whereas an X-Pen is just more adaptable. Also, don't build a second floor. These are big rabbits and a second floor would need to be very sturdy. I originally did it, but realized it was a great pain and for me harder to clean.
The important thing in your enclosure is to know exactly how much out time do you plan to give your rabbit? if it's not a lot, then the bigger the cage the better. If they will be mostly free roam or have a lot of out time then the enclosure doesn't have to be as grand and be used more like a den. When mine we're in their NIC cage I built it 8ft by about 4ft and they loved it. A bit too much since they would hardly come out of it, and it was placed in a dedicated room. Now they are in something smaller, a 5ft by about 3ft walled off laundry closet which in my mind might be all right for just one but a bit snug for two, but they are going to be free roam so space is not limited I feel.
Good luck. My Flemmies have been an absolute joy and by far the best pets I've ever had. Though their destructive capability is incredible if you don't keep their potential for it in mind.