Tom,
Is there a way I can choose whether to edit the jpg or raw version of my file? I now have to change preferences every time I want to switch. Also, (even better) I'd like to be able to choose the raw converter to use.
You can assign a specific editor for each file type we support. You can even add additional editors that are not associated with any specific file type. See the Files tab of the Preferences dialog.
As for choosing which half of a RAW+JPEG pair to edit, you can hold down the Option key (on Mac OS X) or the Shitft key (on Windows) and the opposite half of the pair will be edited. I suggest setting the preference like you have done, but set it to what you want to edit in general, and use the Option/Shift key when you want to toggle the setting dynamically.
To get the most control over the launching process, you can right-click on a photo and use "Edit Photo With" to choose your specific editor from the list of assigned editors. Remember to hold down the Option/Shift key to toggle the setting when you pick the editor from the submenu.
HTH,
-Kirk