Update:
I've got a draft electronics panel with all the ethercat stuff working with linuxCNC, including the servos which i'm able to jog around, which is a great start! it'll be a while until they are mounted physically on the machine, but i want to get started better understanding the process of tuning them, specially since i'm basically blocked from continuing with the physical part of the build until a few more things arrive.
I was able to get the stepperonline software running on a windows 10 vm within qemu and perform the inertia autotune part( which i'll obviously have to do again when they are really mounted ). I understand after that comes a manual part in which you tune the gain along with other stuff, basically testing movements and see what minimizes the error, but i've no idea about how this is done concretely, like what steps in which pieces of software, and specially how it is done for the 2 motors that share an axis.