Once you have created the custom theme and copied it into Recite CMS' themes directory, you can use it on a per-brand basis.

When you're in the Recite CMS Administration Site, open the brand you want to use theme for, then choose to edit the brand. You can then select the theme from the respective drop-down.

Once you save the changes to that brand, all users will automatically see that branding when they log in to clients belonging to that brand.