Either approach can work. Since you've already combined the imports of several Excel files into one FileMaker File, it will be easier to use import records to move selected columns of data from the existing table into new related tables. This can be another table in the same file or a new file.
Thank you for your reply, I figured out how to create the new tables and move the records from one table to another via importing.
My follow up question is what is the best way to remove the duplicates. Since it was originally a flat file, some of the same information is in the new tables. I want to figure out the best and easiest method to remove the duplicates.
The best way is to filter out the duplicates during importing.
Take the key field that is getting duplicate values and specify field options of: Unique Values, Validate always. Then, when importing, you'll get just one record for each unique value in this field.