Make sure you have the supercard patching software.
You can download the programs
here. Make sure you select the proper program because if you download the software for the cf version it will not work.
After making sure that your SD card is formatted in FAT (using your SDcard reder in windows, right click on the drive that is your SD card and select 'format', then make sure it's set to FAT, not FAT32 and format. MAKE SURE IT'S YOUR SD CARD FIRST. This will erase everything on the card, so make sure it's the card and that you don't have anythig important on it.
First, I suggest you download the latest firmware and upgrade your supercard. Under the supercard SD picture there's a file labelled 'kernal 1.60, download that and put it on your sd card, insert it into your supercard, load it in GBA mode, run the file and DO NOT TURN OFF THE SYSTEM WHILE IT'S DOING IT'S THING. that's very important. Let it finish, it will tell you when, then turn it off, and delete the file from your sd card.
Next, load the supercard patching software and you should get an image like this:
Mines a little goofy but you get the idea.
From there click the add button and select your favourite GBA and\or NDS games and once youre done (making sure you right click on the DS games and change the properties to 'SD card'.
You then patch the files, they should end up in the supercard directory in a folder called 'out', unless you specify otherwise.
then you can transfer the files onto your sd card, pop the sd card into your supercard, and run GBA games normally, or pop the superpass into the ds slot of the ds and run ds games that way.