I'm getting ready to upgrade to 5.0 when the BTO version becomes available.  As I've been researching, I took a little time and looked at other "Case Study" websites on ProductCart's website and noticed that many of them, not all, have set up their content like this:

http://www.storename.com/shop/pc/home.asp" rel="nofollow - www.storename.com/shop/pc/home.asp > home page - redirect from http://www.storename.com" rel="nofollow - www.storename.com
http://www.storename.com/shop/pc/viewcategories.asp" rel="nofollow - www.storename.com/shop/pc/viewcategories.asp > as you'd expect a PC page to be
http://www.storename.com/shop/pc/unique_to_industry_info_page.asp" rel="nofollow - www.storename.com/shop/pc/unique_to_industry_info_page.asp > non cart related page

I've been developing with ProductCart since 2008, but mostly with 4 sites from the same client.
I've always laid out my sites like this (non-cart content in root):

http://www.storename.com" rel="nofollow - www.storename.com > home page
http://www.storename.com/shop/pc/vewcategories.asp" rel="nofollow - www.storename.com/shop/pc/vewcategories.asp > cart pages only in this directory... (in "shop" dir)
http://www.storename.com/unique_to_industry_info_page.asp" rel="nofollow - www.storename.com/unique_to_industry_info_page.asp > all custom, non cart content in root

With this structure, I have 2 copies of header.asp and footer.asp, one of each located in the root directory and shop/pc/ folders.

Anyway, I'm wondering what people's thoughts are on these two different ways of setting up ProductCart.

I'm thinking about switching to the first way shown above, because my current site has several different, involved css dropdown menus.  Converting it to Bootstrap is going to take some time.  Moving it all to one folder will be easier to maintain and upgrade, I think...

This question is kind of vague probably - I'm just looking for opinions.

Thanks!!!