Qsys Component Editor for Custom Logic

This tutorial here:

http://www.alterawiki.com/wiki/using_the_usb-blaster_as_an_sopc/qsys_avalon-mm_master_tutorial

Uses the Verification Suite Avalon-MM BFM for simulation stimulus generation, and the JTAG-to-Avalon-MM bridge in hardware.

You can use that to test your own custom logic in simulation and then hardware (where you can Signaltap II trace your design).

Cheers,

Dave