Erm...to my knowledge, wiiflow doesn't support emulated savegames (at least: not yet). As such, the savegames are still on the NAND (say: the hard disk) of your wii.
The best way to copy them is to use a program like
savegame manager gx. I haven't put up with the versions, but it allows to copy all your savegames to your SD card.
To copy them from your SD card to your new wii, you might want to create a savegame for that game first by playing it (start a new game, create a save file, quit), and then overwrite it with the savegame from the SD card.