Hello,
to my opinion, there is no basic difference between Altera FFT core and Matlab FFT function. Matlab is a powerful tool to evaluate different signal processing techniques for a particular measurement task, you can change parameters and display original and processed signals easily.
I agree, that amplitude spectrum (or power spectrum) is a first choice for displaying signal characteristics. It can easily be extracted from complex FFT output by calculating the square sum of real and imaginary part for each frequency and throwing away the upper half which is identical to the lower after this processing. For an linear amplitude scale, calculate the square root for each component.
If the signal is nonzero outside the FFT interval (most likely it is), windowing prior to FFT could be necessary to improve frequency respectively amplitude resolution.
Regards,
Frank