I know we've all been using the Auto-Focus (A/F) for a while, but I never had luck with it (I normally use a Bahtinov Mask), but last night I used it again just to see how it's behaving.
I was surprise how fast it did work. Very nice!

Using the Bahtinov Mask, I have a spreadsheet where I enter the focus position for each filter then calc the offset for each and enter those in the "Filter Setting" icon.

Questions:
1. Do you just check the A/F check-box and it will move the filter to the "Flat Focus Position" it found?
2. Do you A/F all the filters? Or just the first position and the offsets take care of the rest? Or does the A/F do each file that is Checked in the Filter Setting screen.
3. What happens when there are no large stars to A/F on? This morning after a Meridian Flip, I had to move to the large star Gienah, A/F and move back to the Eastern Veil.

I see Jasem's video on it (it's old, 4+ years, but it does have some info on it) Part 7: Filter Wheels

I'll try and answer your questions:
1. The A/F checkbox, when checked, means that when that filter is selected it will trigger an autofocus run. If not selected, it won't. The "Flat Focus Position" doesn't really work. It stores, in effect, the result of the last successful focus run for that filter. I think the idea must have been that if you also check "Capture flat frames at the same focus position as light frames" then when you take a flat on that filter it should adjust focus to the "Flat Focus Position" but this doesn't work - at least for me.
2. Personally I have A/F checked for all filters. There are 2 modes of operation: run autofocus for each filter when that filter is selected; or for example only focus on Luminance and use an offset. So, for example, if Red is locked to Luminance with an offset of 10 and Red has A/F checked then when the Red Filter is selected: Ekos will swap to Luminance, do an autofocus run, swap filters back to red and adjust the focus position by 10.
3. There are a couple of ways to use autofocus... use 1 star and either select it manually or let Ekos select it, or use multiple stars. I use multiple stars. Ekos uses as many as meet the criteria set and averages the HFR. The stars do not need to be "large". If there were stars prior to the MF then it should be the same stars after the MF. Could be that the target is getting lower in the sky and there is more noise so autofocus struggles. You have to play around with the parameters a bit to give yourself the best chance of detecting stars. For example, make sure the exposure / gain is enough. So Lum might be say 1 second, RGB 2 secs and Six/Ha/Oiii 5-10 secs.

Hope this helps!

Thanks for the Check-box info, I had noticed the Ha and Oiii filters I A/F'd on where check when I looked... it seemed to do this on it's own.

The Eastern Veil didn't have any stars that it thought were good enough to focus on. I did cheat before the night's session by focusing on Gienah just above the Veil's, then moved back and started the session.

I did the cheat on a whim because I just wanted to test the current state of the A/F. And since I'm using a refractor, the donut issue I had back with my reflector shouldn't be an issue of course. The process took 30 seconds, very nice!