A big change related to tracking is that when you turn on tracking on an angle it now creates 3 individual track objects. The angle object is "attached" to the tracks but apart from that the tracks are relatively independent from it. For example if you delete the angle the individual tracks are not deleted.
If you double click on the search rectangle of one of the track it will open the right-hand side pane on the Tracking tab. There at the top it will say something like "Angle 1.a" or "Angle 1.b", that's the name of the track. You can click on another track and it should switch to it. From this panel you can change the search window and object window sizes individually for each track (this wasn't possible before).
Previously the tracking of angles and other objects like line, human model, etc. was using its own code and was less accurate and less configurable than bare tracks. Many people used multiple track objects to emulate this (from right-click > Track path). Now the two systems have been unified. Tracking on objects is now basically a shortcut to manipulate the attached tracks at once. This means you will also see the "trace" of each point because it's drawn by the tracks.
There are probably more options that should operate on all tracks at once. The tracking menus when you right click a track are for that track alone. The tracking menus when you right click the angle are for all the attached tracks (start/stop, delete end of tracks, and delete tracks).
I am not sure what you mean by "It picks one, and that's the only marker I can alter.". If your experience is not as above please link to a screenshot or describe the unexpected behavior.
