Assuming that you have Letter Heads:
1st Letter Head (DEFAULT)
Big Header with logo and words + Footer
2nd Letter Head
Small Header with logo
3rd Letter Head
Header with letters only + Footer with ‘printed by computer/ERPNext’
Because the default Letter Head is selected before processing the user has no option of selecting a different one unless after processing Payroll and as to be one by one …
My advise is to add Letter Head on Processing Payroll where the user can select the Letter Head for the Slips before processing or Submitting the Salary Slips.