The 2Gb limit is a limit of FAT16. This was replaced by FAT32 in Win95OSR2.
When you run fdisk, does it ask you if you want to enable large disc support. If it does choose yes and you can set the partition sizes to what you want.
If you reformat in future you are still likely to need to reload though as most applications load settings into the registry (and shortcuts into the start menu/desktop) and this will be replaced by the reload.