Depending on your situation, there are a couple of possibilities.

Example 1:
One benefit (like training) is paid at a different rate, but other benefits (vacation, sick time, etc.) are paid at the normal pay rate.Add the benefit as a separate line to the Employee Pay Rate screen with its own hourly rate. Each employee will have two hourly Pay Codes: one with their normal position and rate (like “Teacher”) with the benefit box checked (to pay vacation, sick time, etc. at the normal rate) and a second line just for “Training”.

Example 2:
All benefits are paid at a different rate (different from the rate for hours worked).

Create a Pay Code (like “Benefits”) and assign it, as a second line, on the Employee Pay Rate screen. Place a check in the Benefit box for that Pay Code. The employee will have two pay codes, one for “Teacher” and a second for “Benefits”. All benefits (vacation, sick, training, etc.) will be paid at that rate.