All you do is create a layout. In that layout you set the panels you want and how you want them. Repeat for any additional layouts you wish to have.
Then as you make different profiles you pick a layout for that profile. The layouts are on the left side menu near the top. just expand the section and you will see the layouts you have created. Select the one you want for the current profile and click the activate button.
Your selecting the layout for a particular profile, not a particular panel. Ill try and show what im talking about in some screen shots when i get a chance if you haven't got it set up by then.
--EDIT--
Here are the screen shots.
This one shows the overall layout section and creating a new one:
This one shows activating a layout:
This one shows the profiles section:
Note that the layouts and profiles are separate. Within my current profile (called shiny in the picture) i can activate any of the layouts i have created without the need to make a new profile. If your using the exact same layout in both cases and just need 2 profiles for a switching addon (like reflux) then you just activate the same layout in each profile. If the layout varies slightly then you activate the appropriate one for each profile. Once activated for a profile the addon will always use that particular layout for that particular profile.