Hi Kevin,
With the manual dispersion function in ISIS you double click either side of each line in the uncalibrated (combo) spectrum and ISIS calculates the exact pixel position of the centroid of the line and enters the value in the table. You have to tell it to look for either an emission or absorption line within the two clicked positions though (buttons at the top of the window) so you would need to click “absorption” before measuring the water line positions and “emission” before measuring a lamp line.
Yes, if you set the reference line to 0,0 it just uses the predefined dispersion equation but if your dispersion was measured on a reference star with the telescope pointing in a different direction to the target, this can be out by a constant shift due to flexure so adding a reference point using a lamp spectrum corresponding to the target will correct for this. (correcting the constant in the polynomial)
Robin