What are "joints"?
..are you maybe asking about how the join the rafters to the ridge board? Using Coping tool (Modify tab) with a Coping Distance of 0'-0" for the rafters.
Is that a Beam System controlling those upper beams (the squares)? If so, you will need to move the Beam System element (the dashed lines which show up when you hover your mouse over the top of one of the small beams) rather than moving the individual beams. To do this, align the Beam System element to the "main beam" below it: this will make your beams in the same plane as the main beam. Then move the Beam System element away in a perpendicular direction from the main beam a length equal to the depth of the beams in your Beam System.