It looks like the Leadshine 1-channel EtherCAT steppers export the Z wire as the 31st digital in pin (0x60fd:00, bit 31). Odds are, the 2-axis models are the same. In theory you could handle it in software, but only when moving at slow speed. At anything over ~15 RPM you'd probably miss the marker between servo thread ticks.
You could probably do a fairly nice 2-phase homing this way -- home with a switch, then back up slowly until you find the Z marker, and now you're accurate to 1/4000th of a rotation or so. That'd be great if you wanted to make a bunch of very small items with very high repeatability. Like dentures or something

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In any case, I don't think you *need* the Z bit. Like Rod says, you probably don't really need an encoder at all, but it's nice to have. Since you have encoders already, it's probably worth getting closed-loop drives and the voltage shifter that you'd need to make it work.
I should mention that I don't think anyone has tried to get the 2-axis Leadshine drives to work yet with LinuxCNC. They shouldn't be *that* hard, but they're in flux right now. You could probably clone a 1-axis Leadshine generic XML config, adding 0x800 to each PDO address for the second axis. Or you could wait a bit (days? weeks?) and the CiA 402 driver should support it. I had a 6-channel EtherCAT stepper driver appear in the mail today (thanks DSS!), and I'm planning on ordering a 2CS3E-D507 once the lunar new year festivities are safely in the rear view mirror. So in a month or so, there's a pretty good chance that the Leadshine drives will just work out of the box.