Where can we install mods to keep them seperate?

[Stealth2668]

Now that mods can be separate for organization, can we put the whole mod folder in the KSP folder or do they "parts for example have to go in the "parts" folder of KSP still (KSP > GameData > Squad > Parts)?

Thanks.

[IllicitMedic]

For mods that have been updated for 0.20 simply drop the entire mod folder into the GameData folder and your done.

Mods that have not been updated yet still use the old file structure to install mods.

[Stealth2668]

ok thanks. Hopefully mods will be updated soon, don't want clutter

[EndlessWaves]

do they "parts for example have to go in the "parts" folder of KSP still (KSP > GameData > Squad > Parts)?

No, the only thing in the squad folder should be squad parts.

Other than that you should be free to organise them within GameData as you like.