This mostly applies to a user on a Mac, as it has floating windows, and on Windows BaseElements starts up maximised.

If you move and arrange the windows as you work, but want to get back to the standard arrangement, there is a script in the "Scripts" menu to do just that on a per file basis. There is also a script in the BaseElements file to re-arrange all of the windows at once.

Moving all the windows at once.

If you move the BaseElements.fp7 window to the new location you want all of the windows to appear, you can then get all of the other windows to move to this location. Just run the script "Set Window Positions Current Window", and all of the windows will be moved to match the top left coordinates of the current window.