MakerBot Print is our newest print-prepration software, which supports native CAD files and STL assemblies,
allows you to interact with all your printers via the Cloud, and many other exciting new features.
In Cura you can use the Tweak At Z Plugin. It's under "PRESETS", and is pre-loaded on the IIIP version, not sure where in later versions.
You just add a Tweak At Z layer for each temp change, then enter the new temp for each layer.