this is for a university assignment - I have to use eps files
If the assignment is to create a 2-color separated workflow then it's hard to find a problem with eps other than it's an old format. EPS vs PSD output is easy enough to test by placing the same file saved both ways, and sampling the separation values via Separation Preview. You can also check the output values in Acrobat by exporting to PDF/X-4. Acrobat's Output Preview's Object Inspector shows the two formats as having the same resolution and color space.
For CMYK and RGB workflows EPS does have a problem with downstream color management, but in the case of duotones in a separated spot color workflow there would be little need for additional color management other than an attempt to proof the job to a composite printer. Even for proofing it's hard to see an advantage to PSD because you still can't include a source profile for spot color.
You do have to wonder about saving to .ps—exporting to PDF/X outputs the correct separation. Maybe it's a history lesson?