I've never used wacs but checking the doc seems you can specify the store with parameter --certificatestore and use My as certificate store (in the doc it says it is the Personal store).
If left empty, certificates will be installed either in the WebHosting store, or if that is not available, the My store (better known as Personal ).
So if you issue your certificate adding this it should add the cert to the right store:
--store certificatestore --certificatestore My
Keep in mind I did not test it so if you have some doubts maybe you could open an issue to validate the right conf to solve your problem or you can wait till some community buddy with wacs knowledge take a look to this post
Thank you for your reply but I believe that is a Global setting. So you can either store in Personal or Web Hosting but not both. I want the web sites in Web Hosting but just this 1 in Personal