If you've set up to manage a multiple brand Zendesk in the Enterprise version of Zendesk (see Setting up to manage multiple brand Zendesk accounts), you need to run Chat from the hub Zendesk not the spoke accounts. This is because the agents who solve tickets are in the hub, not the spokes.
You can still provide Chat to your users in the spoke accounts, you just have to generate the Feedback Tab code in the hub Zendesk and add it to each of the spokes.
Chat is enabled as a feature of the Feedback Tab, so there's two steps to set this up. First, enable and configure Chat and then enable and configure the Feedback Tab to include Chat.
To configure Chat in the hub Zendesk
Sign in to the hub Zendesk as an admin. If you're using Enterprise or custom agent roles (see Custom agent roles), any agent that has permission to set up Channels can also perform this task. Zendesk's predefined roles of Administrator and Advisor both have these permissions.
Click the Manage icon () in the sidebar, then select Channels > Chat.
There are lots of options for setting up the Feedback Tab. How you set these is up to you. The option that is relevant to this task is End-users can chat with Agents?. Set that to Yes.
When you've finished configuring the Feedback Tab, click Preview and grab code snippet.
Note: On the Feedback Tab Settings page there is also a tab called Advanced Customization. This is where you can brand the Feedback Tab. However, since the Feedback Tab will be used by all of your spoke accounts, you should leave the default settings as is. In other words, don't add any branding.
Select and copy the code snippet.
To add the Feedback Tab to each of the spokes
Sign in to each of the spoke accounts, one at time, as a user with permission to add extensions. Zendesk's predefined roles of Administrator and Advisor both have these permissions.
Click the Manage icon () in the sidebar, then select Settings > Extensions.
Zendesk Classic: Select Settings > Extensions.
Enter a title for the widget (for example: Feedback Tab).
Set the Available For option based on how to want users to access your Zendesk.
Paste the Feedback Tab code you copied from the hub Zendesk.