I see this very old post, tho will respond to help for anyone curious.

The junctions are modular like stations. You place it, and then can "Configure" it like a station.

Pick streets or tracks and place them over the existing streets and tracks you wish to replace. It is possible to make many varieties of mixed configurations this way, like track + street below and only street above.

Initial settings when placing are very limited, tho this is merciful because so many options are possible that the menu would be very long and laggy.