Installing a mod on a minecrat server is not a hard process but you have to proceed carefully and step by step.
Note that many mods are NOT multiplayer compatible and can be installed ONLY for single player mode (eg not on your server).
Among the multiplayer mods a few are compatible with craftbukkit, most are not.
Note that mods require a client side installation as well.
If your mod is forge compatible (most common situation):
- make sure your server type is set on "ForgeMod" in mcmyadmin > configuration > server settings
- stop your server
- download the Forge mod on your pc and rename the .jar file to ForgeMod.jar- upload the compiled ForgeMod.jar by FTP on your server (overwrite existing one if any).
- start your server and test
- upload your forge compatible mods into your server "mods" folder. The "mods" folder should be created after server first start on ForgeMod.
There are other server types available:
Basically you need to repeat the above steps but set the server type and rename the server .jar accordingly:
Official: Your .jar file must be named minecraft_server.jar (that's only if you run in vanilla mode, without any modification)
Tekkit: Your .jar file must be named Tekkit.jar
Feed The Beast: Your .jar file must be named ftbserver.jar
Spigot: Your .jar file must be named Spigot.jar
Tekkit Lite: Your .jar file must be named TekkitLite.jar
Forge Mod: Your .jar file must be named ForgeMod.jar
Craftbukkit: Your .jar file must be named craftbukkit.jar
MCPC+/Cauldron: Your .jar file must be named mcpc-plus.jar