Download the resource cd from here (http://www.terasic.com.tw/cgi-bin/page/archive.pl?language=english&categoryno=139&no=502&partno=4). You may need to register.
I'm sure the H/W connections are fine - I'm not doubting the jtag connections.
The base address is specified when you put your Qsys system together and instantiate the EPCS - assuming that's what you've done. Based on the fact you're trying to use 'nios2-flash-programmer' I hope you have a Nios in your system and an EPCS.
Download the CD and look at some of the examples - there are quite a few you should be able to look for guidance.
Cheers,
Alex