I had the Ishar games back in the day when I owned a 486 and even then they were a pain to get running properly, but I hoped that the GoG release would allow me to finally enjoy them with all bells and whistles. Tough luck, it isn't happening.
First, no matter what setting I pick in the graphics setup dialog, the game runs horribly slow. It takes approx. three minutes from the time I double-click "start.exe" to see the language selection screen. I clawed my way through the intro sequence (with the wizard going "poof" and the doors opening) only to see that the main game ran even slower.
And to complete my woes, there's no sound in any of the three games. Everytime I start one of these, I get a deafening "crack"-like noise, as if an old Soundblaster would lock up and then nothing.
Before I get "look at the FAQ" - I did just that. I fiddled with all the settings in the graphics setup program AND I tweaked the config files for all three Ishar games, but to no avail. My rig couldn't be to blame. I just did a fresh system install yesterday (otherwise I would have tested the Ishar games with my own DosBox install) and I think an AMD 64 x2 with 3 gigs of ram should easily be able to get the games running at a steady pace.

You can run the graphic setup tool for each of the games from the start menu folder, no need to browse to the game dir to do that.
And yes, all gog games should (in principle) be fired up using the shortcuts gog's installer places on your desktop.
Anyway, you got it working now and that's what really matters. Have fun.

Hi, I recommend to use some grafic frontend of dosbox, e. g. D-Fend Reloaded, and then in profile editor of game to set "CPU emulation core" to value "dynamic". And you can edit item "Grafic" as you need, too.