AI Search tries to find your website's existing search box and open over it when a visitor clicks it. On a custom theme it may not recognise yours. Here is how to point it at the right box.
Tell it which element is your search box
Add the attribute data-mando-search-trigger to your search box element (or the icon that opens it). AI Search then opens whenever that element is clicked. This works however you installed AI Search.
If you run search through your AI agent
When you chose Run search through your AI agent instead of pasting the code, you can also fill in the Search box to take over field on the Deploy step with a CSS selector for your box. That field only applies to the agent option; if you pasted the code snippet, it does nothing, so use data-mando-search-trigger instead.
Good to know
If AI Search cannot find any search box and there is no fallback button, visitors have no way to open it. Adding data-mando-search-trigger fixes that. To review how you added AI Search, see Add AI Search to your website with code.