I'm confused as you're using SignalTap and Virtual JTAG Interface, which aren't necessarily the same thing(yes, they both use the JTAG hub). I've found the User GUide useful(search on Virtual at this link, and it will have the user guide and the examples):
http://www.altera.com/literature/lit-ug.jsp Also running at a shell "quartus_sh --qhelp" and looking at the available shell commands to be informing. I've gotten by running a Quartus shell and directly interacting with the VJI through Tcl, specifically device_virtual_ir_shift and device_virtual_dr_shift commands. Are you looking for something more low-level than that, so the Quartus shell is not needed? I understand that could be useful(maybe the VJI is part of the final product), but trying to understand. Not that I can make it happen or anything. (File an SR, not that that will do it, but that will show a request for enhancements...)