Sage 100

v2013 - I need to set up payroll for an employee that works in multiple states, what is the best way to handle?

So are you deducting SIT for each state? What about unemployment insurance? What issues are you concerned with?

For instance, employee lives in MA and we need to set up withholding for MA and CT as they work in both states.

Well, you would have to enter a separate earnings code for each states wages and change the state code on the line to that specific state. MAS would calculate the taxes for each state's earnings. Where it becomes messy is if you want to allocate any pretax deductions to each state. I don't think this will work. You only get ONE suta choice so this may be an issue for you.