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Thanks for the info. I got this IAR Systems J-Link (I think it's now Segger, but the one I got still says IAR Systems) that can program a lot of JTAG devices, but Quartus doesn't show it as an option, while it does show the USB Blaster. It'd be good to use J-Link for everything, since it can program the other chip (ATSAM4L), but oh well...
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Quartus Programmer will not show third party devices (other than Altera USB Blaster clones). Most likely the Atmel tool won't as well. The Altera software knows how to read .sof/.pof/.jic (in my case I use the altera tools to convert/embed my .sof file into a .jic file that will be programmed into the attached FPGA flash device).
As I said earlier, you could (probably, altho I have no direct experience with that JTAG device) use the altera programmer tools to build a .SVF file from your device .SOF file, and then your third party tool software that knows how to access your JTAG USB device should be able to replay the .SVF file. Ditto for the Atmel device program and its tools.
PS: In looking at the Segger site, their device(s) look to be oriented to be JTAG debuggers for embedded microprocessors (like ARM, etc). Not a general purpose JTAG device. That being said I suspect their device is physically capable of replaying an .SVF file over JTAG (it is just basic JTAG protocol), but I did not see any mention of that in their software functionality. So no joy for that device, I guess.