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TheBlackOmega, sorry for delay, just saw your post today.
I'm using Cura, which does not require M280 and puts the T0/T1 tool change in when needed.
I used the below:

Extruder 1 End Gcode: G1 X150.00 Y160.00
Extruder 2 End Gcode: G1 X130.00 Y160.00

I did this due to use of a Prime Tower roughly 20mmx20mm at fixed location of X140.00 Y160.00. This way when the carriage moves to the Prime Tower at the end of the tool change, the new nozzle will be in the middle of the Prime Tower (at the fixed location, which is also in the slicer). Then as it starts the Prime Tower (from the middle/inside) it wipes the nozzle and leaves any extra crap in the middle of the tower. Sorry, I don't have experience with Slicer and dual nozzles and tool changes, but hope this helps.