You connect two GBAs with a link cable, one with your Gen2 game and the other the transfer ROM. Through some witzardry, you actually REMOVE THE ROM CART. From there, it's as if you were trading Pokemon!
Here's the video I found that goes in depth on it!
www.youtube.com/watch?v=m7mU...
youtube.com
Sending Pokemon to Gen 3 on REAL HARDWARE!
YouTube video by Skul