You should probably replace everything.
You can leave your products database in tact and keep all of your uploaded images, but you will have to remove the different color options that exist and re-do those with the prostore v2 admin.
You can probably save a copy of your template and relavent css files to restore those as well once updating the entire site.
I'd probably do a dump of your current products table so you don't lose that data, and back up a copy of your current site.
Then start fresh with powerstore v2 and get it working as-is.
Then copy back your images and restore your products database and make sure it all still works.
Then copy over your template and .css files and use DW to update all of the pages using your customized template.
At that point you should have the new site with your customized template and existing products and images.