We have been running the Build process at the Message level in order to see the changes in our Message Scripts as we go. This may be considered good practice (particularly when first starting out) as any discrepancies can be discovered & rectified as you go (in potentially fewer, smaller batches). Once you are more practiced and confident in the accuracy of your configurations, you can run the Build process at the Integration level. This means that the process will cycle through all the Field records on each of the Messages on the Integration in turn & auto-generate all the relevant Message Script code.