There is a fundamental difference between having a moving tool for Y axis travel, or moving the work piece past the tool.
Having a moving work piece changes the orientation of the tool path display so everything is backwards compared to the default configuration.
Can there be a selection for tool travel vs work piece travel? 
On my machine the Y axis is set up for Y+ moves the work to the front of the machine, Y- moves the work to the back.

Always think in terms of the tool moving regardless of what actually moves.
Then set up the machine motions so that the display matches.
It is just a matter of selecting the correct directions in axis movement and homing.


Mike

That sounds terrifically obvious, but I see that in reality that's not what I've been doing. Because the work moves for Y axis, I think in terms of moving the work when I write the G code. I will try to change my thinking along these lines and see if it makes it easier.
I have the axis directions reconciled with the display, and arcs and circles move in the correct direction, so it's just me that needs adjustment.

A few adult beverages can make the adjustment go a lot smoother!
Have fun with the machine.

WARNING
Never drink and drive your machine.


Mike

I can't even contemplate having a few doses of vitamin R and being in the same room as that machine.
I have, in the past, actually made errors while under the influence. And I learned from that.
If I can prune a finger nail with the mill while cold sober, I'd take off a couple fingers after drinking anything.
I will share this in case it helps someone.  I just got a new milling vise and promptly peeled back an inch of skin on a finger by bumping into a raw edge of the thing.
Freshly milled edges are sharp ridiculously sharp.