It looks like G54 and G55 are used on CNC machines for changing coordinate systems. Interesting that it would show up on a 3D printer.
There are several options.
You can code a post-processor to insert those commands after T0 and T1 commands.
You can set the Printer Settings, Extruder *, Extruder Offset settings. This won't actually change the coordinate system, but it will make Slic3r pass offset coordinates depending on the active extruder.
Depending on your firmware, you may be able to set the firmware to handle the offsets.
RepRapFirmware has the ability to programmatically run arbitrary gcode when specific tools are activated or freed.