When I hove with them mouse over it, both tracks are colored blue in the 2D height view. However, upon click only the top most track is selected.
one of the techniques is to create dedicated layers for each loop and show/unlock only the layer that is currently worked on.
In order to select arbitrary tracks the 'Walk Selection' feature can also be used, i.e. from the currently selected track element the Select > Select Previous (Next) Track menu command can be used to move the selection to a track in the loop (or elsewhere).
The 2.5D view can help visualizing where the selected track is located with respect to the overall helix.
Hope this helps,
Wouldn't it be a good solution if track selection is also possible in the 2.5D track view?
From the selected track you can continue selecting a range of connected tracks using Shift;
We've prepared a little video demonstrating the technique.
Depending on what you're trying to achieve you can e.g. repeat these the steps to assign each loop to a specific layer (Layer > New Layer from Selection) and just work on these tracks, etc.
Indeed, and it's a topic on our to-do list to be added in a future release when we get a chance!