Limits are configured solely to limit the amount of registrations coming through the Online Registration website.  However, there may come a time that you will need to manually pre-register someone in the HCR.  You will want that manual pre-registration to be counted against the caps you have configured for your Online Registration so that you do not go over your limits.  You can configure a participant's preregistration record that was added manually in the HCR to respect your configured limits in Online Registration.

Since limits are configured on the Division Mappings of a package, a participant's preregistration record contains options that allow you to select which package they would have chosen if they did it online.

On a participant's preregistration record under the Pre-Registrations tab on their profile, you'll find the Online Registration portion of the registration itself. Choose the package for which this registration should respect its limit(s) in the drop-down labelled Package.  Because a Package can be configured for multiple Division Mappings, you must also choose the appropriate Division Mapping for which the registration should respect its limit(s).