bukkit isn't a plugin, though there is a little unknown secret to help.. if you drag and drop a .jar file onto the main launcher window.. it will create a .bat file (with the same file name as the dropped jar file) in its installed directory.. if you run the .bat file it will use whichever java version u have selected in the 'Java Settings' to launch the dropped .jar file (something I made because I mainly use java portable).. you can even edit this bat file yourself to make other changes.
autocraft.. dunno what kind of mod that is.. if you are wanting to install mods forge/litemods, they all just go in the 'mods' folder of whatever modpack you installed (every modpack makes its own folder in the main launcher directory to avoid clutter, in there you will find the 'mods folders... I have made 2 modpacks that include forge and litemod, 1.7.2 and 1.7.10 ie if you downloaded 1.7.10-LiteLoader from the modpacks, it would have a folder with a mods folder inside where most client mods can be installed ie "1.7.10-LiteLoader\mods"
if you want to go install all mods yourself including modloaders like forge/litemod etc then you are on your own. It is still possible with my launcher, just helps if you install the kzsetup as it puts the launcher in the .minecraft folder.. which is where modloader installers like forge/litemod generally look first to to install there stuff because that is where the official launcher goes.