Not sure about this one:
In indi-eqmod, you can set the coordinates of the telescope in the 'Site Management' tab.
However, on restart/re-connection you have to enter the values again.

Are the values saved automatically or do I really need to enter them each time?

Under "Automatic Device Updates" in KStars Options --> INDI, the Time and Geographic options are by default true, that is KStars sends the driver the current time and location automatically. Therefore, just set your site to whatever you're using for EQMod and it will be set automatically. Another option is to disable those two checkboxes and enter them manually in EQMod.