It's confusing because some of this logic is in the mount firmware, and some is in Ekos. This means the specifics are different for different mounts.
At least for my mounts (iOptron, 10Micron), it's not "side of pier" but rather "hour angle" that triggers the flip. There are two interacting pieces of info:
1) The mount firmware (not Ekos) normally slews to locations from the west side or the east side (of course!) depending on where in the sky its target coordinates currently are (azimuth). There is a "gray zone" very close to the meridian which ca be set in the hand controller to allow a slew-from-the-west to a point just before the meridian. I usually set this gray zone to be very small -- for me, 1 degree. If Ekos triggers a slew to any point west of that gray zone, the mount will approach it from the west.
2) In Ekos there's a setting to perform a meridian flip at some hour angle past the meridian. This must be set AFTER the "gray zone" set in the hand control. In y case I set this for 1.5 degrees past the meridian.
The usual series of events is
a) Mount tracks past the hand control gray zone (hour angle = +1 degree) while exposing an image
b) Mount tracks past Ekos "Meridian Flip" limit (hour angle = +1.5 degrees) while STILL exposing image, sends message "Meridian Flip Waiting"
c) Ekos completes current image and downloads from camera
d) Ekos sends command to slew mount to current target RA/DEC
e) Mount flips in order to approach target from the west because it's west of the "gray zone"
f) Ekos does an "alignment" step using plate solving to re-center target
g) Ekos begins exposing next image in sequence
The critical thing for me is to set the gray zone in the and paddle to be smaller than the meridian flip angle in Ekos.