I'm not sure I understand what you are asking, but here are 2 methods I use:

1. You can rearrange items in the left-hand structure page by simply clicking and dragging.

2. To rearrange buttons etc. on the menu page, just click/drag them around on the menu page so they are in the order you want. Then you must rearrange the linkage between them.

The way I do it (there may be other/better methods) is to click on the Navigation Tool button on the toolbar. This is the one with the arrow pointer above the link symbol, just to the left of the Preview button. Clicking that causes curved arrows to be displayed on each of the 4 sides of the selected button. Each arrow points to the button that the menu will jump to when you push L, R, Up, or Down on the controller.

Notice that each arrow starts from a small triangle on the side of the selected button. If you click on this triangle you start a new/replacement arrow that you can drag to where you want to arrow to point. This will re-establish the destination for that directional key on the controller.

I've not used themes myself by my guess is if you refresh the theme it will reorganize everything the way it wants, and not how you want. In general themes are best used as starters, but once you start customizing or changing your layout you are on your own from then on. If you refresh the theme or invoke a new one you will essentially be starting over from the theme's design, not you modified one.