I know I felt a little overwhelmed by all the boxes at first. But just spent some time customizing my home page, and really enjoyed it. Now my page looks the way I want it to look!
What I did to make this easier for myself is open up the NGA on 2 different tabs, one on the 'customize home page' page, and the other on the NGA home page. Then I could play around with the boxes, then click on the NGA home page and see what happened to my home page as I moved the boxes around. I was finally able to settle on an ordering that I like.
But to get your watched threads from the bottom of the page to the top, just find a little box that says 'watcher notifications'. Move that little box up a larger box in the very top row.