If you don’t have prior data in Initiative Tracker, download data.json and paste it into your .obsidian/plugins/initiative-tracker/ directory, replacing your existing one if necessary. If you do have prior data, open .obsidian/plugins/initiative-tracker/data.json and copy the contents of pf2e-conditions.json into the statuses array. If you don’t have a statuses array, add one after the homebrew array.
Open Obsidian and go to Settings > Initiative Tracker. Verify that you see conditions with the PF- prefix in the list of conditions.
Open the Initiative Tracker pane and add combatants.
Click on the HP of a combatant to open the HP dialog.
In the second field (marked with a tag icon), type PF- and select the condition you want to apply by hitting the ENTER key.