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I tried tutorials but it doesn't run as wanted, maybe a version difference or maybe it's my fault. I'll try another time tomorrow...
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SignalTap II? I use it all the time with various version of the tools and have never had a problem.
Synthesize your design, then start SignalTap II, add signals to the SignalTap II instance, setup a clock source, setup the number of samples to capture, save the instance, add it to your project, resynthesize, download to your board, and then 'scan JTAG chain' in SignalTap II (if it doesn't auto detect that the instance is now valid).
Cheers,
Dave