Unfortunately, I think the program is the only way to mod the game at all, or at least simpler than actually finding the files to replace. The character files for the games are all over the place, I really couldn't make sense of them.
The program is not too complex though. You can unpack it anywhere. Then Run "Skin Installer Ultimate.exe", it should ask if you want it to update and find your game folders, press yes.
The most complicated part comes when needing to add the skin.
Under the Add New Skin tab, on the right hand side of the window are buttons for "Add Files" or "Add Directory". You use those to add the files for only one mod (if you add a .zip or .rar file that contains a patch, the program with automatically look inside these files).
After you add all of the files for the mod, press "Add to Database" below the previous buttons. Make a name for your skin and hit "ok"
Then you go to the "Install Existing Skin" tab, which will now have the skin you added. Mark the checkbox for whichever mod(s) you want to install, and click install (near the bottom, left side of the window). A window will pop up asking you what portions you want to mod, just hit Save.
Then it will ask you which skin to replace, if you want it to replace the base skin of a champion, choose "default". Hit "Done" and the mod will be installed.
That came out a lot longer than I hoped, but if you need more help I'll be happy to.
