OK, I'm going to tell you how I'd do it. It may be possible to do something similar with something fancier, put I don't know of any way to automatically add "some" fields to a table.
FileMaker can add fields upon an Import (or creation). So, what I'd do is open the Excel file with FileMaker. You can either create, a new file, or use the option to add a New Table (Target:) during an Import. I'd just use "Open" and create a new file, because I'm going to throw it away when I'm done with it (and it's less confusing).
You now have a table with all the new fields. It likely also has existing fields. So you view the fields. This next method requires FileMaker Pro Advanced. It allows you to select all fields (on Mac, Cmd-a). Then, holding the Command key, click on the fields you do not want; they will no longer be selected. Now Copy. You can then go to the table you want to add these to and Paste. The new fields have been added to your existing table. (While this works like copy/pasting data, this is NOT data, it is special; it does not go to the "clipboard".)
You now can do an Import Records from the file/table, where you have the new data. Choose "Matching Names" as the option. Once you've got the data, you can throw away the file/table. As you said, the next one is likely to be different.
In both the "Open" or "Import", be sure to click: [x] Don't import first record (contains field names). FileMaker will still be able to create the fields if needed.
I know, this sounds like many steps. But each can go fairly quickly; faster than creating hundreds of fields; FileMaker should get the correct types of fields from Excel.
P.S. I see that you could do the Paste of the new fields right in the Import itself, by choosing the "Manage Database" button (lower right). Also, I do know whether FileMaker Pro Advanced 8 has all this. I no longer have it on this computer.
This method saved me lots of time to import all the field names.