The placement I think is logical - where you have two parts of the whole /body or object/ that you want to move in different angles from their connecting point; But the right deformation depends on more factors than just placing joints in the right position.

I may share what have read so far, as I am coping with the same problems in the moment. Before you start using the Joint Tool, be sure that in the Setting Box is checked the xyz Orientation. Naming each joint right is very important. In case you are making a human, using names as left_wrist or left_elbow is convenient, because then you can use the Mirror Joint Options and replace all "left" names with "right". I mean this creates the other hand automatically.

Next is that you must orient the joints the right way. Selecting the root joint, you can use Skeleton > Orient Joint and most of the joints will be oriented the right way, but still you have to check them manually. All must have 0 Rotation value in the xyz directions.

Hope this helps