There should be no problems running both versions of cura on your machine. I am doing the same because 15.06 led to horrific over-extrusion on the first layer.
The proper codes are already in place, all that is left to fill in are the values which are dependent on the material you are printing with.
For example, I normally print ABS using 250c for my extruder and 90c for my bed. At the end of the print I like to cool the extruder to 150 and the bed to 80. This way it heats up quickly when I start my next print. When the connection to the printer is established I like to auto-warm the bed and the extruder to 150/80.
If you are using an older cura with your settings changed to reprap flavored gcode, you will need to edit the start/end gcode in cura. If you are using the new cura (15.06.x), you will have to enter the start/end gcode into the octoprint gcode script settings.
Of course, all of these scripts can be edited to suit your needs.
-Kevin