There are several ways to make a emu NAND.
If you are going to use WiiFlow to extract your NAND it is recommended that you go to Channels view first before going to config menu to extract your NAND.
WiiFlow NAND extractor makes a full NAND backup including Wii game saves, channels and their saves, SYSCONF, Mii's, cert.sys, and settings.txt. The NAND is extracted to dev:/wiiflow/nandemu unless you edit the path and partition ahead of time by editing the wiiflow.ini under [NAND].
In global settings you can also extract Wii game saves to your NAND. Not needed if you used WiiFlows NAND Extractor since it already extracts them. Best for when you make a NAND with Modmii. You can select ALL or MISSING. You can also go to individual game settings and extract the game save or flash it back to real NAND. The Flash option will only be available if there's a game save on the emu NAND. Extracting and Flashing game saves only works for Wii games.
You can also set how much emu NAND you want to use. In global settings under nand settings set emulation to PARTIAL (GAMESAVE) or FULL. PARTIAL uses the real NAND for Mii's and SYSCONF (controller settings). FULL uses the emu NAND for everything. In wiiflow.ini under [NAND] there's real_nand_config and real_nand_miis. These default to no. They don't do anything with partial nand but in full nand if both are no then you still have a partial nand. I guess they are there in case you use full nand but still want to use one of the two from real nand.
Note: this page is unfinished. Will be working on it soon.