Private conversations can take place on the messages or any of the comments pages throughout the site, using the visibility icons to exclude clients and/or trade partners.
When you post a comment, all of the people on your team who have access to the project and instant alerts for comments turned on will get the notice.
Using the To-Do or Warranty pages you can create a task, assign it to an internal team member and/or trade partner, and add comments. If you hide the task from your clients, they will not be able to see the task or any added comments.
On the Schedule you can add Private Notes that you only want shared with builder side users, or Public Notes that you want both builder and trade partner users to see.