How do I charge researchers (who have funding grants) based on their bookings?

You can make it mandatory for users in your lab to select a funding/grant code when creating a booking. To do this you will need to use the Projects feature, which is available on the Premium and Enterprise Calira subscriptions.
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Firstly, please ensure that Projects is turned ON in your lab's settings. Then, you will need to create the Project with a Funding/Grant code and assign it to your users. Please see the Projects help guide if you require assistance with creating a project.
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In your user's settings, or in access group settings, you can then turn on the rule 'Are funding codes mandatory when creating a booking?'. This will mean that a user must

select a project to associate their booking to before they can proceed with the booking.