I have checked that your downloaded mods with thunderstore are saved here
C:\Users\[YOUR PC USERNAME]\AppData\Roaming\Thunderstore Mod Manager\DataFolder\REPO\cache
Meanwhile the folders for your profiles are here
C:\Users\[YOUR PC USERNAME]\AppData\Roaming\Thunderstore Mod Manager\DataFolder\REPO\profiles
if you select a profile, there's a BepInEx folder. go there, and there's plugins folder. That folder contains all your used mods for that profile. Just not sure on how to manually insert this mod for it to work when you use the profile. Need someone to test it
Okay so you just need to make a folder in your chosen profile, put the mod on that folder, then run the mod using that profile with thunderstore. it will automatically activate the mod
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C:\Users\[YOUR PC USERNAME]\AppData\Roaming\Thunderstore Mod Manager\DataFolder\REPO\cache
Meanwhile the folders for your profiles are here
C:\Users\[YOUR PC USERNAME]\AppData\Roaming\Thunderstore Mod Manager\DataFolder\REPO\profiles
if you select a profile, there's a BepInEx folder. go there, and there's plugins folder. That folder contains all your used mods for that profile. Just not sure on how to manually insert this mod for it to work when you use the profile. Need someone to test it