Hello, Mark. Welcome to FileMaker.
Anything you do on a routine basis is a candidate for automation. First, it minimizes the chance of error. Second, I'm lazy and hate doing more work than I have to.
In a case like this, I presume you have some sort of unique key available for the incoming data? If so, you should be able to use that key to refresh any existing records, while simultaneously adding new ones in either a single table, or by using that key in a final table after you do as you suggest and use a couple of staging tables. Either way, I suggest you write some scripts to automate the task. Include error checking to make sure what you get is what you're expecting (because sometimes data sources can change on us), and allow hold points for you to spot-check the incoming data.
Hopefully, that makes sense. Let us know if you have specific questions.
Mike's idea is what you need to do. Get a script to automate the imports. And if you have FileMaker server, you can schedule the script to run monthly in the evening or some weekend so it is getting work done while you are not.