Does importing with the "update matching" option work for you? A single import can update matching records and create new ones. If there's a creation date field that auto-enters the creation date and you enable auto enter options during the import, newly added records will show today's date in this field, updated records will not.
If you do find that need to go with an intermediary table--this can be needed to process some imports to get issues "cleaned" before sending data to final table, keep in mind that the data in this table should be of temporary nature. once you have processed the data from the intermediary table into the final tables, you should be able to delete all records from it, starting over with an empty table for the next import.
I'm currently using that "update matching" option, and it works perfectly for me and the data. But my users can't seem to get their heads around which fields need to match using the equals sign icon, which can be left with the arrow icon, which field names belong to which spreadsheet column names, and why there are extra fields in the database they should be ignoring. I figured it'd be simpler to just give them an intermediary table with field names that exactly match the spreadsheet column names, and then the script can shuffle the data around to the right tables from there.
The only problem then is that as you recommend, the intermediary table should be cleaned out at the end of each import. Then how will I be able to use the update-matching option, since the intermediary table will be empty? Or is that what the creation date field is for? I'm afraid I'm not quite getting it yet!
You should use a script for importing the data. Then the users do not need to make any decisions about how to match fields for import. At most, they would need to select the script for import when a dialog appears asking them to select a file. The rest of the process should be automatic.
The Date modified field would not be part of the temporary table, it would be a field in the final destination table(s). Thus, this information would be retained when you clear the temp table after processing the imported data into the needed destination table(s).