Hi Tony,
I have a LHIRES III and an ALPY 600. I would not say the LHIRES is more advanced as such, they just complement each other and fulfill different roles. The ALPY 600 is more “fit and forget” and although the LHIRES is an excellent high resolution instrument, the ALPY is easier to use and performs much better than the LHIRES when used at low resolution. In many ways I find that producing good quality spectra can be more challenging at low resolution than at high resolution. (eg the targets are fainter, the sky background higher and atmospheric extinction correction more important)
Regarding rough guides from acquisition to final spectrum, I gave some very general walk thoughs for Star Analyser, ALPY600 and LHIRES using Vspec and ISIS at the recent BAA workshop at NLO Sidmouth, which can be downloaded here
http://www.shelyak.com/dossier.php?id_dossier=36&lang=2
They may not be totally self explanatory though so I am in the process of writing some words to accompany the slides which hopefully should make them more useful
For ISIS, Christain Buil has some tutorials which take you through the steps, though because ISIS is continuously evolving, the current version of the program does not always match the tutorials
http://www.astrosurf.com/buil/isis/isis_en.htm
Cheers
Robin