Some user options (a.k.a. parameters) are initialized for a mouse-driven session. It may be worthwhile to note that Ediff may be customized using ediff-customize.
First, as mentioned by @phils, you should customize the variable ediff-window-setup-function e.g. M-x customize-variable. Set this variable to "Single Frame" by clicking on the button Value Menu, then press the key 2 and finally saves the setting using the button Apply and Save.
The function ediff-regions-wordwise can act on different regions in the same buffer. Therefore, you just need to select the different regions consecutively.
Press C-g if you need to deactivate the preselected region. To mark a region, press C-x SPC to activate the mark and then move the cursor. As indicated, you should "submit" the active region using C-M-c.
Concerning the frame configuration, I think that you should set the variable ediff-before-setup-hook. You may also look at ediff-hook using M-x customize-group.
Note: I find that the user manual is of no help for your issue. It may be worthwhile to know that C-u M-x ediff-windows-wordwise compares the windows without user selections if the frame already contains the corresponding windows.