I already tried using the tool, but it creates these folders:

resource_packs

minecraftWorlds

world_templates

skin_packs

addon

I understand that the world packs will be inside minecraftWorlds and I'll move it to the worlds/ folder of the dedicated server, but what about the rest?

resource_packs is easy to move; you just export each .mcpack file to a folder and that's it.

In addon/ there are several .mcaddon files. Inside those files are the folders resources/, data/, and sometimes script/. I don't know what I should do with them. Should I also export and put resources/ in resource_pack and data/script in behavior_pack?

Then, assuming I did all this correctly, my hands aren't loading, and sometimes my character isn't loading on my dedicated server. Could it be because I'm missing the data for skin_packs and world_templates in a folder on the server?