Once you determine where a painting takes you, click on that painting's box to set the stage. You can set the stage either by clicking on the stage from the list, or by typing in the stage name and pressing Enter to autocomplete. This will make some icons appear next to the stage:
Clicking the painting itself will toggle the row as completed, eg. once you've gotten all the stars you want to get there.
In addition, there are Mips and Toad icons next to some of the floor names, so you can check off each Mips and Toad as you collect its star.
As you fill in the painting destinations, the Loops section will automatically populate. This shows you which stages will loop if you keep re-entering the paintings. For example, if the BoB painting takes you to CCM, the CCM painting takes you to LLL, and the LLL painting takes you to BoB, that creates a "loop" and you'll see it in the Loops section.
If a loop requires you to enter a different painting than the one you exit (eg. exit DDD, enter BitFS) then you will see icon with an arrow, telling you to leave one painting and enter another.
Only the main stages are considered for the Loops section, as you wouldn't want to loop many times into a bonus stage with only one or two stars.
Click the Popout button to use the tracker in a popout window. This website will remember your popout window size if you resize it. Making the popout skinny enough will move the icons below the stage instead of next to it, which can help fit the tracker in a stream layout.