Currently the plugin does not support having both Skills (as they are in default RPG Maker) and Cards at the same time as the plugin converts all Skills into Cards. You can invoke Skills independently of the Card System using the Force Action function or through AI commands using plugins like YEP Battle AI Core.
We are working on an extension plugin called Party Battle Type C that will allow the entire party to have a single Deck which seems to be in line with what you are trying to achieve with this battle system (where the Deck is based off their inventory). We will let you know when this extension is complete and available for download :)