I assume you are removing your card because you have a new one. Just take the card out, put the new one in, and install the new cards drivers. Removing the old cards drivers is ussually not nessicary, but sometime will cause issues of all shapes and sizes if it is not done. Follow bob's how to for removing the card and then do that in reverse for the new card, remember to clip it in.
You didn't need to format your comp, and a card in the AGP slot is not an integrated card for future referance.
Use the CD that came with your new card to install the drivers manually, then download the latest version of directX and the latest card drivers from the website of your graphics card manufactures (Nvidea website for geforce, ATI website for radeon and soforth). This MUST be done before any of the newer games will run properly. I know that for a fact because I updated to a 9800 pro just recently and tested with farcry before updating my drivers just for the heck of it. Crash city.