so, standing facing the router, X going left to right, and Y going toward/ away from you, home is at 'away,right', correct?
if so, then you have your router set up according to the industry standard for mills.

now, X+ moves left to right, and Y+ moves away, and Z+ moves UP (all tool motions).
all correct so far?

you need to set your work co-ordinates. What software are you using to run the router?

Here is Universal Gcode Sender as an example (if the router is controlled by GRBL)


I have clicked the 'machine control' tab.
The buttons 'reset X axis' 'reset Y axis' 'reset Z axis' each set the relevant axis to '0' at the current location in the current co-ordinate system.

What is the current co-ordinate system?
There are 6 of them, set by G54 through to G59. G54 is the default.

At the LEFT hand side you can see a display of 'work position' and 'machine position'.

Let me try and tie it all together:

• Machine position: physical co-ordinates of the machine, it uses this for homing etc, and all internal measurements like soft limits.
• Work position: where you are on this part in this program. This is applied internally as an offset from the machine position.

Why 6 of them?
So you can have up to 6 vices or other clamping positions on the machine, and load up to 6 pieces of material at the same time.
For each vice or fixture you set a work co-ordinate system 0,0.
Then you can run the program 6 times, just giving the G54 (run program), G55 (run program), G56 (run program) and so on to switch from vice to vice.

How to use this?

1. home your machine as usual
2. clamp your material anywhere on the machine. front and center will do fine.
   
3. jog to the left hand edge (or wherever X zero on the material is)
   
4. click 'reset X axis'
5. jog to the front edge
6. click 'reset Y axis' (as above)
   
7. jog Z to the surface of the material (if using material top as Z-zero)
8. click 'reset Z axis'
9. run the program

Now the Gcode programs +X and +Y movements can happily move right(x) and away(y) on the part, and -Z can cut into the material, just like on every other CNC machine on the planet (-:

Some web references to expand on what I have explained:
http://www.tormach.com/g54_g59_g59p.html
http://www.cnccookbook.com/CCCNCGCodeTouchOff.htm
http://www.cnccookbook.com/CCCNCGCodeG54G92WorkOffsets.htm
http://wiki.linuxcnc.org/cgi-bin/wiki.pl?CoordinateSystems
https://github.com/grbl/grbl/wiki/Frequently-Asked-Questions