If the only thing that you need to do is add new records, this is relatively simple to do. But if you have records in the master database that need to be updated because values have been changed in the on location copy things get a bit more complex.
And if one user might update a record in one fashion in the master copy at the same time that another user might update the same record in a different way in the "on location" copy, things can get very complex.
If you just need to add new records or if you do not allow records to be edited in the master copy, only the single "on location" copy, then Import Records in a Script, is the best way to go. And matching up fields in the field mapping dialog should not be a major problem as long as you maintain identical names in the source and target tables of each import. That allows you to make a single selection: "Matching Names" from the arrange by drop down and all fields in the source table match to the target table by field name.
For more on "synching" FileMaker database files, see: http://www.filemaker.com/solutions/ios/docs/fmi_guide_sync_en.pdf
And you may want to evaluate a 3rd party tool specifically designed to facilitate synching two or more copies of a database. Both SeedCode and 360Works offer such products so you can google those two companies and see what they have to offer.