The answer is the bonuses work for all ships under them in the system they are. Extra task forces are useful if you would want a fleet for patrolling/defending(1) colonies as well as separate fleets for training(2) and attacking(3). Task force 1 would focus on political relations (public affairs) more than other fleets because they will be the ones with guns (no rhyme/creation of band name intended) over the heads of possibly billions of your own people, as well as focus on fighters (Fighter Operations) and missiles (logistics) so that task force will have the best in those areas. Task force 2 will be away for longer that most training in various systems across your empire (RP, it can be in any one system) so it would need officers with the highest training value that are free (Operations). Task force 3 will be general purpose and will need the best officers available that TF1 doesn't have ie communications, logistics (50:50 importance with TF1), and intelligence. TF1 officers would most of the time be on a colony and would be in a flag officer transport for short journeys to neighboring colonies, TF2 officers would almost always be in a transport with the training ships, and TF3 officers would always be on their mighty flagship that is protected by many other ships at a front-line base. And it is (mostly) for RP purposes. You can add task groups to a task force in the task group order menu (under the location of the task group, and you can transfer locations (colonies) by having a transport with a flag bridge over their location and using the Move to flagship drop down (then click save), move the ship to what colony you want, then the Move to Population drop down when over a different colony (click save), or to a command-ship/flagship (ship) by skipping the last two steps (all in the task force window).
http://aurorawiki.pentarch.org/index.php?title=Leaders