Simulation of a Qsys system with external logic (Modelsim ASE)

I already read Altera AN351 to get the functional simulation of a Nios II based Qsys system running a given user program. I'm now trying to find out if is there any way to simulate the same Qsys system running the same user program but within a larger digital system with user external logic added.

Thank you for any help you can give me.

Regards,

Lorenzo