Where's the problem, actually?
In my experience simply formatting the SMC with the GP32 works best. When I tried to format it with a card reader on Mac OS X (using "MS-DOS format") it worked fine but transfer speed went down, slow as molasses, apparently OS X can't handle the format it just created itself. Weird. Formatting it with Win98 worked fine as well, but then OS X couldn't read it at all. And at the end of it all I got a totally corrupted SMC, with the GP32 crashing when "getting smc size" as PCLink reported. I had to use the commandline tool (maclink format) to format it again, since that was the only tool that simply sent the "format" command to the GP32 without trying the lethal "get smc size" routine first.
Bottom line, use the GP32 to format an SMC, period. Even with FAT12 I can use long and mixed case filenames just fine, on both platforms (Mac/Win).