Yes, you can.

You can manage multiple Shopify stores from a single vwa.la account if, those stores use the same email address. You can then manage your influencer marketing program for both stores from the same vwa.la user account. Simply log in, go to your dashboard menu and then select the store you want to manage from menu as below:

How will billing work?

Due to the way shopify billing works, each store that you install is managed as a separate billing agreement with Shopify.