Now, as for linking with nodes – that is not supported at this time. Is this your primary question? I’m going to assume that it’s the main issue you’re facing and turn this into a feature request – at the moment, there’s no way to define relationships between Table Wizard-managed tables and tables integrated with Views by other modules (such as the node table). Supporting that will take some work…
via Allow relationships to other views-enabled tables | drupal.org.
OK, so we imported CALI Lessons into Drupal as nodes. Now I’ve got the table that tracks when folks run those Lessons. It has about 4.4 million rows and contains what is effectively relational data: ids for Lessons, People, etc, and run data: time of run, questions answered, etc. So we were hoping to use Table Wizard to surface the data in Views2 and combine it with Lesson node info to produce nifty pages for people to see the Lessons they have run. But as noted above TW doesn’t support building relationships between TW-managed tables and existing Views tables, so no way to link the nid in the LessonRun table with the nid in the node table or the uid in LessonRun with the uid in the users table with the nifty Views2 interface. Looks like I’ll just need to code it in.