To keep branded versions in one prototype, I would create an initial branching page (e.g, “Home” in the sitemap) with buttons or a droplist for each “brand”. Choosing a brand (clicking a button or selecting a list option) would set a global variable to that brand name or identifier. Each page would then have an OnPageLoad action to test this global variable and set things accordingly.
To make it easier, put all the “branded content” on each page in a dynamic panel (or set of dynamic panels if they are in various locations on the page) and add a state for each brand. If it is something common to all pages, such as a logo image and/or page header, create that as a Master and deploy the Master to all pages. Put the OnPageLoad event code in the master so it can take care of itself. As a simple example, with ACME1 or ACME2 as the only choices, and different logo images being the only difference, I would assign OnLoadVariable to a value of either “ACME1” or “ACME2” on my Home page. Then in my master header/logo, use OnPageLoad to set the panel state to the value of OnLoadVariable (making sure to name my states the same as the possible values.)