Changing the logo for the affiliate panel is simple, just open your merchant panel, go to Configuration ->Design, and there you can upload your new logo.
If your logo image is bigger than default read here.
Changing designYou can change the design of the affiliate panel by editing its templates. PAP uses the Smarty template engine, so it should be easy to edit the templates.
For example, if you want to change the header of the affiliate panel, you have to edit the template file:
There's also easy to use tool for quick template changes in merchant panel in Configuration -> Affiliate panel tab Customize design.
There you can edit the appropriate template with one click.