Yes it'll run that way, but watch for air trapped in it. On mine, a small section must've had air trapped. When I tipped the box one afternoon, I could hear a bunch of air hit the pump. As this was the two day test before the mobo and componenets went in, it was the perfect time to work out these details (and the trapped air).
It didn't cause any real problems, it just made me wonder if the trapped air could've effected cpu temps. I'd bet yes.
I'd recommend that once you get the system filled and your still in the testing phase, dismount the rad and turn it over when the pump's running, just to make sure all the air makes it out. Once this is done, it shouldn't become a problem again unless the system is emptied for some reason.
Have fun!
