SMRT Link is the web-based end-to-end workflow manager for the Sequel®/Sequel II System. It includes software applications for designing and monitoring sequencing runs, and analyzing and managing sequence data. SMRT Link provides a web interface that can control multiple Sequel/Sequel II Systems.
SMRTtools are command line tools that are used by SMRTLink. People who are command line savvy can just use these, if you don't have a need to control a sequencer.