(Current for KSP version 0.25)
Certain tasks in Kerbal Space Program, like installing mods and flags, downloading vessel files from this site or elsewhere, or moving vessel files between your saved games, require access to KSP’s root directory.
If you installed KSP via Steam, you may find the root directory by opening Steam, then going to your Library. Find Kerbal Space Program, rightclick it and choose Properties. Under the Local Files tab, click Browse Local Files. This should open your root directory.
If you had installed KSP manually, the root directory is either KSP-win, KSP_linux, or KSP-osx, located wherever you unzipped the archive to.
You know you’re in the right directory if there is a KSP.exe in it with a rather familiar icon.
Henceforth the root directory will be designated by “%root%”.
To add mods: You need to copy the mod’s folder from the archive into %root%/GameData . Read any readmes or FAQs about the mod for the details. Note: never delete the “Squad” or “NASAmission” folders. It is also a good idea to back up your saves when changing mods, especially if the mod contains vessel parts.
To add flags: Create the folder %root%/GameData/customflags/Flags. Move any .png file here to use it as a flag. For best results, size it to 256 × 160 pixels. You can also view the default flags in %root%/GameData/Squad/Flags .
Manipulating vessel files: Under %root%/saves , there should be a folder for every game profile you have. Within these, your vessel files are found in the Ships folder, in either the VAB (for vessels built in the Vehicle Assembly Building), or SPH (for the Spaceplane Hangar). To use a downloaded vessel, you need to put the downloaded .craft file in the corresponding folder.
Back up/share saves: Easy; just copy the game profile folders to a safe place (you can also put them into a zip file). Note: never delete the “training” or “scenario” folders.