Set up separate work areas for discussion and posts of work as a project or team assignment progresses. Final projects or assignments may be posted to a separate discussion board where all teams post work in a completed state.
Make team discussion boards that have explanatory titles, so the entire class has some information about what each team is working on. Specific titles also make the discussion more navigable.
It is difficult to ask students to change the subject line with each message, but you can make the subject line for your initial messages as specific and clear as possible, with the most explanatory power. In one case, a professor was successful in asking students to append the subject line to make it unique and easier to find; as the discussion grew and messages became numerous, they found the added effort worthwhile.