In our setup there are two websites. One for B2C, and one for B2B. Since B2C was the first one created it's header/footer were set as default for customer preview of quotations (the ones that are viewed using button in email "View Sales Order").

Neither of those websites had the header/footer we wanted to be shown to customer when they preview/sign orders using customer portal view. So we created another website that only had desired header/footer for our customer preview. There is no way (at least we didn't find it) to select header/footer design for customer preview. Sure, you can set prefered website on contact (customer profile) but in most cases when they click on link that is sent via email they will be logged out and header/footer will be from the site that was created first (in our case B2C). What came in my mind was that those websites have some kind of index and sure they have - their order can be changed through menu (that I was able to find only when writing it down on home screen) 

Write down 'websites​' and click on Website / Configuration / Websites

Here you can set the order of websites, the first will be used as default one for those who are not logged in. If you have better solution please share the knowledge.