Well it is almost sorted out on this side.
One of the reasons why I don't use the IDE is because my clients all know RS232. The cable is simple and the interface reminds all of a telnet session. Many times the NIOS board is so hidden away, far, far down in a box with the operator sitting somewhere on the outside, like in a military tank application. So far I have had bad experiences with JTAG cables of 5 meters and usually the ByteBlaster must be within centimeters from the FPGA. With serial it is slower but much more flexible. Another reason to use the serial cable is that a MAX232 contains 2 channels. On many applications I have 2 windows showing diagnostic data. But many prefer to step through software. If you cannot program then it is your problem. I like to code, download and run. Been programming since 1981 and the more complex the tools the slower the development (in the beginning it seems faster).