Tandem Y Axis in stepconf assistance.

I have spent quite a while trying to get one of our older CNC's to run again. I had a lot of issues with getting the gantry properly setup and I heard that 2.9.4 has support for tandem motor pin outs so I downloaded it and I have managed to get the gantry to move. The problem is that if i'm in the test axis in stepconf only 1 motor moves and in the actual jog interface the motors are separate joints so if I jog the gantry then I have to jog joint 1 and then joint 2 instead of pressing one button. As a result I move it incredibly slowly to avoid skewing it as much as possible. I would imagine I did something wrong or that their is some way to combine the two joints too run at the same time? would I need to do this in the HAL or INI files?. My other question is about how i'm supposed to setup the limits because I have just been setting up as: both limit X, both limit Y, and the same for the other two motors. I did get an error about limits on one of the Y's  but it didn't say much other than something along the lines of "Error limits Joint 2"
www.probotix.com/CNC-ROUTERS/CNC-ROUTER-GX2525 Here is the machine (It only says Comet on it but I am very sure this the same one)
www.probotix.com/wiki/index.php/Unity_Controller  Here is the controller its using as the old one had some fried chips that couldn't be replaced. It also has the pin outs where I got the limits from.
Sorry if I it's something obvious because I really haven't used linuxCNC ever before (Also disclaimer: I haven't set the latency test right yet because I only got it working in a test setup yesterday and I didn't have time for it but I know I need to do it)
 

Well it has 2 motors and the web page mentions that it needs limits/homing switches because of the tandem setup. Each motor for the gantry also has its own cable and port. I am assuming thats what drives are.

I would imagine that it does. All the documentation suggests so and from what i can see on the other side (Its right up against a wall) It looks the same on both sides so I would wager it has them on both. So im going with yes on that.

Read the online documentation for V 2.9  for "homing configuration" (Several times)
the HOME_SEQUENCE parameter for each side of the gantry must be the same and it must be negative to tell Linuxcnc to treat it as a joint axis.