The Questions:
1) Am I going about this the wrong way? Should I not use a form and/or upload the excel file?

Well, not the necessarily the wrong way (TMTOWTDI and all that), here's an alternative approach:

1. Provide an upload widget for the user to upload the Excel file
2. Spawn a seperate process that will parse the file (see Spreadsheet::ParseExcel) and update the MySQL database
3. return a message to the user letting them know their request is being processed

HTH,
Ian