yes, you should create on your sd card a fat partition, and an ext4 (or ext3, shouldnt matter)
then install your fresh nand build, and it will autodetect the ext partition and treat it as phone memory, leaving the fat partition to act as the 'sd card'.
so, when you instal an app, install uit to phone, not sd card, and it will actually end up on the ext partition, and the phone will treat it as if its in its internal rom.
When you browse with a filemanager, you will not see a seperate ext partition, because it is integrated into the system, but you will see an sd card listed, which is the fat partition.
The other plus side is when you install a different rom, when it boots any apps found on the ext partition will already be installed.
This all happens automatically, so long as you have an ext partition, and a rom that supports it. you do not need (and nor should you) go into teh app settings and choose move to sd card. if you do that it will move to teh fat partition, which defeats the object.