You can be logged in with multiple accounts simultaneously. In the add-on sidebar, go to Data source, and select the data source you need log in with. If you are already logged in with one account, you can log in with another one using Switch: Add new account. Don't press Log out, as that will erase the authentication information of your other account:
When you run new queries, they are always ran using the credentials of the user you have active in the sidebar. Afterwards, when the query is refreshed, the add-on will try to continue using those credentials. But if that account has been logged out of in the sidebar's Data source tab, then the add-on must use the credentials of the currently active account, if you are still logged into some AdWords MCC.
To make it easier to manage multiple accounts, we have recently added a "Refresh with user account" parameter to the SupermetricsQueries sheet (scroll to the right end). If that parameter has a value specified, our add-on will primarily try to refresh the query with that account's credentials, provided that either of these conditions apply:
The query has been refresh before with the specified account, and the user who did the refresh has not logged out of the account, or
The active user (Google Drive account) is logged into that account in the sidebar's Data source tab