Disclaimer: I've only been using this software for a very short time, so I might have well missed seeing what you need.
My humble opinion:
Although you can add HTML to your shopping cart pages, there's nothing that I can see in either version of Shopping Cart Designer that will make it easy -- you'll have to hand-code it. I don't see a way to include meta tags inside the header, which is where they need to go. You'd probably have to do that outside of Coffee Cup, after designing the cart or shop.
A lot depends upon whether you use the your shop's Home as the actual home page of your site, or if you have an existing website with a link to your shop. If you have to jury-rig something into an existing page of Shopping Cart Creator's output, you'll have to add that code every time you change your shop. If you add it to your 'regular' home page, it will remain independent of the shop.
To make this a little clearer, imagine that I have an website called 'widgets.com', and I want to add a shop to it using SCC. I build the shop and upload it to my server, and put a link to it on my home page.
The original website lives at '
www.widgets.com' and the shop created by SCC is found at '
www.widgets.com/shop'. SCC is responsible for all of the files in the shop folder, and I have free control over my homepage, which is
www.widgets.com/index.html. It is in that file that I include tags for search engine optimization.
Doesn't mean you can't do it within the Coffee Cup app, but I imagine that it's a lot less straightforward to pull off and would get pretty messy.
All this is leading up to: I think the safest thing to do would be to obtain the HTML Editor and do your work with that, and to put the meta tag keywords in your index.html file rather than trying to fiddle around in SCC's output.