Where in the software do I indicate that I want to pay 990-PF depository taxes?
All depository taxes for a 990-PF return must be paid using the Electronic Federal Tax Payment System (EFTPS).
For more information about EFTPS, or to enroll in the program, visit the EFTPS Website, or call 1 (800) 555-4477.
Refer to Publication 966 and the Form 990-PF Instructions.