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That's exactly what i did but it returned me an error when i selected run as NIOS II hardware, eclipse told me that the port was already in use by another program or something like that.
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Ah that might be because Eclipse and Hyperterminal are both trying to use the port. What you could do is use nios2-download from the command line to download your code and then use hyperterminal for the standard in/out. When you download via Eclipse it automatically opens the console which is most likely conflicting with Hyperterminal.
By the way I used to use a program called brayterminal (sp?), it was lightyears ahead of hyperterminal so you might like it better. I don't know if it's around still though.
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