So far I aligned my EQ6-R mount manually with the handset before switching to kstars, but I recon this is not the way to work properly.

When I setup my telescope it is obviously roughly pointing at Polaris and I would assumed doing an alignment with sync at the beginning would be fine, but Ekos says, Sync error.

So I wonder, what is the proper procedure to get going?

There isn't one really besides the mount being in the home position (i.e. roughly looking at polaris) in most of the cases. I haven't used hand-control in years. Usually, I'll slew to some bright stars, then focus, then run alignment and that's it.

Ok, then I was not so way off the right solution. I will try next time.

I need to get a direct cable for the EQ6-R mount as well, so I don‘t have to set the handcontroller to PC direct mode.

I'd highly recommend that.. maybe the problems you've been experiencing are partly related to PC direct mode.

I agree. I also ordered a Raspberry Pi and will move the indiserver there. Together with the G-Photo driver that should be way more stable.

I have one additional questions about the startup coordinates the telescope is pointing at.

When I startup the telescope for the first time in the night, it points roughly at Polaris. So do I set these coordinates as Parking position and Indi will overwrite the telescope's internal settings upon firing up like date and time?

When for some reasons (like my Canon freezes again) I need to restart INDI again in the same night, the telescope is pointing somewhere and I usually want to take the coordinates from the telescope and update INDI with it. How do I do that? Or is this done automatically?

Thanks in advance