In my experience, just consider the zero point to be the default software starting position when you run EKOS. I'm not sure about this but this may not be true if the motor has encoders.
Starting from zero can be a bit annoying at times, Say your focuser is already near the focus point. If it starts at 0, it will have no valid inward travel steps available.
In that situation, I use the Sync box under the focus driver's Main Control Tab to give it some arbitrary higher value.

I would recommend you rack he focuser all the way in. Sync it to zero. Focus the telescope on the sky and note the position.
Save that position as a preset in the INDI driver. Now the next time you start from zero and fully racked in, you can call upon the preset to get a roughly accurate focus to begin with.

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