To mod Minecraft so, you can go to appdata\roaming\.minecraft, and then, instead of going to the "bin" folder, you have to go to the "version" folder.
You should see all of the versions that you have downloaded on the new launcher (i.e, 1.6.1, 1.5.2, etc.)
What you have to do is make a NEW folder, and name it anything you like, such as "Modded", or "yugewfkqegyvfqbvkyefve".
Then go into the "1.6.1" folder and copy all of the items inside. You should notice that there is a .jar in there.
Paste those items into the folder that you just created and rename them the same name as the folder.
Now open the file labeled as a .json (Modded.json, 1.6.1.json, etc) in Notepad, Notepad++ or any other text editor.
Then, next to the id, where it says "1.6.1", you replace that with the name of your folder.
Then you mod the .jar in your folder however you wanted to mod the minecraft.jar.
You open up your launcher, create a new profile, and under "version", there should be a version with the name of your modded folder.
You run that version, and you're done!