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The main tool is STIG.pl. You run perl STIG.pl {--check|--fix} <benchmark-xccdf.xml> --out <benchmark-results-xccdf.xml> on the machine you're checking.
Most of the time, you have to specify a profile with --profile <profilename>, but it will tell you that when it parses the XCCDF file.
If you run it without arguments, it prints out a usage message.
The other interesting option is --log <logfile.txt> which keeps a log of the messages that get printed when you run the program.
Any files that are changed by the fixes should be backed up in the backup directory under the hostname and date.