Yes you can do that. You will need to create a custom income category at the company level with a "Type" of "Per Mile" and then apply this new income to your employees.
Please refer to our Quick Start Guide with step by step instructions on how to create a custom income type.
Payroll Mate Quick Start Guide can be accessed from the link below:
http://www.realtaxtools.com/pm-quick-start-guide/pm-full-tour.pdf
Real Business Solutions Support Team, Makers of W2 Mate and Payroll Mate
708-479-8731