The software we use to go from STL files to the X3G files that are used by the Replicator is "ReplicatorG" with the Sail Fish modification.
http://www.makerbot.com/sailfish/install/
Sailfish firmware adds velocity profiling to the Replicator, so it prints faster and with better quality. If you have two nozzles (we do), it also adds "ditto printing", which allows printing from both nozzles simultaneously. This lets you print two parts at once, if they are smaller than the spacing between the nozzles.
The options for rafts and support structure in ReplicatorG are tricky and finicky. Unfortunately, they don't always work as advertised, and you need to experiment with the settings and part orientation to get things to work right. The software uses the last settings as the default for the next part, so in that sense, it is "automatic", but I believe the installed default was with rafts and support structure turned off.