(General) Changing / modifications isn't really something for this topic.
So you'd probably be better of asking these questions in a new topic.
But I am happy to give you some info, which might help you getting started.
To change the way the template is build up, you should make your own templates.
Like the browse_color and flypage_color templates are added in these color themes.
Simply copy and paste the template you think is most close to what you like.
Then alter this one as you see fit.
Did you try to set the browse_color and flypage_color templates yet?
They might give you a headstart.
These can be set under the VM admin:admin
tab > ... browse
The cool black frame:
Shows only when you go into product details:http://www.silksbyelizabeth.com/silk.html?page=shop.product_details&flypage=flypage.tpl&product_id=18&category_id=6
Maybe it is possible to change the templates, so that this is always the case?
I didn't check if it is hardcoded, else compare the codes in both templates.
But is more a question to ask in a new topic.
"How do you get the shopping cart button check out feature to show up?"
You can approach this in many ways..
You can make a menu link somewhere to the cart;http://www.silksbyelizabeth.com/index.php?option=com_virtuemart&page=shop.cart
Or after adding something to cart, you have the pop up window, which has a "cart"link as well.
When you have a new template files, I think many people will appreciate it if you share them / make them available to the public.
All these although linked, aren't dedicated to the color_themes, so please ask follow up of these questions in new topics.
Off course are questions / information directly linked to the color_themes welcome. Good luck.