It's not the same thing.
Basically Sonic & Knuckles had an additional cartridge slot. It looked like this:
http://upload.wikimedia.org/wikipedia/commons/4/43/Sonic_&_Knuckles_Genesis_Cartridge.jpg
Now, if you inserted a Sonic 2 game into this, you could play Sonic 2 as Knuckles.
But if you inserted Sonic 3, not only could you play as Knuckles in Sonic 3, but it linked the levels in Sonic 2 and Sonic 3 into one long game.
When you played it this way, if you collected all the emeralds (in order to become Super Sonic), at the end of Sonic 3/beginning of Sonic & Knuckles, you lose the Chaos Emeralds and they become Super Emeralds. If you collect them all again, throughout the Sonic & Knuckles levels, then you can become Hyper Sonic who is even more powerful than Super Sonic.
Super Sonic is yellow, Hyper Sonic is a white/really light blue color.