This is mostly based on Fetish's workflow guide in the MoonGlasses Discord
When you create a mod project using the Toolkit Editor, it automatically saves the project in the following path:
Baldurs Gate 3\Data\Mods
This makes it available for the game to load directly. This is convenient, but can also lead to some problems if you publish your mod as a .pak file to the following path:
AppData\Local\Larian Studios\Baldur's Gate 3\Mods
Having both the mod project and the .pak file will cause conflicts. This can lead to issues when playing your mod in the game, such as the mod failing to work correctly or at all, even if it works perfectly in the editor.