if you can get the towers on points the first night and cash with points the second confirmed when you make the reservation it should not matter. if you can confirm the points night first and have to wait to confirm the upgrade on the paid night or want to save ( because an upgrade at the hotel is 1500 and is 2500 in advance ) then i would do the points first.
If you do pts the 1st night and $$ the 2nd, will you still get a stay credit for paying the 2nd night. I imagine that paying the 1st night 1 will get the stay credit. Any time I added to my res the hotel simply bunched it all together into 1 res although I had 2 different confirmation #s.
So if the Hotel does that and my 1st night is a free 1 then it will all show up as a free 1 and no credit for the 2nd night.