On Confluence Server, Custom Charts will automatically link to the Primary Jira connected to the Confluence instance.
Only the Primary Jira will be used and it is currently not possible to select an alternative if multiple Jira instances are connected to Confluence. If you require this additional functionality please contact our support team to discuss this feature.
Custom Jira Charts for Confluence Server & Data Center can only be used with Jira Server & Data Center instances.
Jira must be connected to Confluence using OAuth (impersonation) and the usernames must match exactly on both instances for Custom Charts to function as expected.
A detailed description (with screenshots) of how to correctly configure the application links can be found here: Server - Application Link Set Up
On Confluence Cloud, Custom Charts is connected to Jira instances individually by each user.
This means that each individual user who creates or views a Custom Jira Chart will need to authorize the app to connect to a particular Jira instance on their behalf.
In reality, this is very easy to do as most users will only have one Jira instance associated with their Atlassian account, so it is the only option in the drop-down list during authorization.
This is a limitation that Atlassian is planning to resolve in the future by allowing admins to have more control over user connected apps on their instance: https://trello.com/c/3KDefQjC
Custom Jira Charts for Confluence Cloud can only be used with Jira Cloud instances.
A detailed description (with screenshots) of how to connect Custom Jira Charts for Confluence Cloud to a Jira instance can be found here: Cloud - Connect to Jira