If I signed my bosses name on A/P and payroll checks while she was sick and she was aware of me doing this, was it a crime?

This could be considered fraud, and even "uttering and publishing" if these checks were ever presented to a financial institution to be cashed. The issue is whether or not you were acting as an "agent" on behalf of your boss, and within the capacity of an agent or representative, your were authorized to sign her name onto these checks. If so, then I doubt any criminal charges will issue. If not, then the issue will be whether or not your boss wishes to press charges against you for fraud or uttering and publishing.