We pay proportional taxes on the % of income that comes from other states. For example, if 80% of our revenue comes from Illinois and 20% from Michigan--we only pay taxes on the 20% from Michigan.
"Doing business" (as far as our accountant is concerned) is having billable clients in those states--generating revenue. We've had employees in 3 states (MI, IL and FL) and the only concern is making sure you are meeting that states payroll tax and withholding policies.
On a related note: Some states have different workers comp laws. We we're not required to carry workers comp in Illinois, but did need it in Michigan (and we also had to insure our Illinois employee, because she was now working for a company that was based in Michigan).
It's a confusing mess sometimes--seek help from accounts and lawyers and don't be afraid to call the state and just ask.