just fitting one so question is what do i do with the pipe that ran from the old airbox to the rear of tank then to the crankcase???

That pipe is your crankcase breather. Ideally, use the stock oil separator box. It will increase the apparent crankcase volume, and is better for adding some torque, and giving your bike better breathing. The stock fitting on your engine does not have a reed valve in it. The only change would be to add a one way valve coming out of the oil separator box. While the stock hose went to the air box, it is better if you let that go to the atmosphere. there are lots of nasty acids and chemicals in that mix that you don't really want to put into the intake. By using the stock oil separator box, you keep the oil from getting your bike dirty. The K&N will just dirty your bike, and not give you very good breathing.

Here are a few articles for you to read, if you need some other opinions.
http://www.ducati-upnorth.com/tech/breather.php
http://ducatimonsterforum.org/index.php?topic=2469.0
http://www.britcycle.com/products/bunnb ... rticle.pdf

i bought the KrankVent, and it works well, though not cheap.
http://www.et-performance.com/kv.html#M ... &_CRUISERS

Your stock airbox is also best, with some better breathing in the lid.

If you have the stock oil separator box, keep it. Just add a one way valve to it and vent to the atmosphere.
That's my opinion.

Cheers,