Hello Siu, thanks for asking!
You shouldn't edit the files inside misago directory at all, unless you want to maintain your own misago fork (that is custom version of Misago).
Instead, you should use the theme/templates directory created for you when you run misago-start.py for first time. Inside it create the misago directory to tell Misago that you want to override its html with custom ones. Then in that misago directory create the navbar.html file to tell Misago that you are overriding default navbar with your own. Open this file in your favorite code editor, and edit it to look like this. After that you will have our own navbar.html file that you can customize as you like.
I understand that this may be an overkill for people who just want to add custom link to menu, and ion future Misago versions I will be adding more admin options for customizing theme without the need for editing any files.
Lastly, I have moved this thread to category dedicated to discussing customizing the way Misago looks.