Programming in C under Win98

I have Win 98 and FAT32. Can I use MS Visual C++ 6.0 to compile, link, debug and run from source code with the extension “–.c”, although the compiler declares:”Copiling 32-bit module”, and –.c programs run under dos and 16-bit file system? Do I have to format the drive with FAT and use Win95 instead of Win98 because I am getting compiler errors even with the sample code provided by the manufacturer?