Copy the zip file into Documents\EmoTracker\packs and then restart EmoTracker.
Click the items in the Items window as you obtain them to track them as collected.
Right click the question mark spaces in order to set each dungeon's reward. You can choose to mark them as the vanilla pause menu layout, or to mark which dungeon has which reward. Hovering your mouse over each question mark will tell you which dungeon it represents.
NOTE: When this tracker was first published it was a map tracker. The map location data, while obsolete and very out-of-date, still exists and can be restored to the tracker via removing the comment indicators from various lines in tracker_layout. You will also need to change the allow_resize option from false to true. The legacy map tracking instructions are below.
When you first start, set the open door / open forest / goal conditions at the bottom left. These affect what locations will show as available. Also set which medallion or stone you got for free. The order of the medallions and stones don't correspond to the pause menu but to the dungeon locations. So once you find out what you get from the child dungeons, mark the three at the bottom even if they're medallions.
The maps are split into child and adult, with child on the left/top and adult on the right/bottom, depending on your layout.
Dungeons will not show as full clearable until you obtain all the keys for them. Double-click a dungeon location to pin it so you can track the keys as you pick them up.