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](https://emacs.stackexchange.com/a/51429/19761), 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 <kbd>Value Menu</kbd>, then press the key <kbd>2</kbd> and finally saves the setting using the button <kbd>Apply and Save</kbd>.

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-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.