You should be able to hover over the menu, and when the box appears there is a square node on the top center. Click and hold that node while dragging up until the items are centered.
Thank. I did the dragging which does not align my menu items with the logo, instead it put the menu at the top.
It's hard to know what the exact issue is just from the screenshot. But I often use this code in css to have columns align in the middle vertically:
Place that in the column housing the navigation.
Navigation can be finicky, so I won't promise that will work for you in this case.
It should not pop to the top! It should be draggable throughout the column. If you are not able to do this, you need to open a support ticket within the editor and let Duda Support help you. All widgets can be moved up, down, left and right.