Since emuNAND is basically a copy of your 3DS's sysNAND, when you system transfer while being on emuNAND, the copied information in emuNAND and your eShop information will be sent over to the New3DS. Your old 3DS's sysNAND is still in firmware 9.2 with some things intact (like previous eShop purchases and stuff), but on emuNAND it'll be like as if you're setting up your 3DS for the first time after it was formatted. Oh and your eShop NNID account will be linked to the New3DS so when you try to get on the eShop on the old 3DS, you can't re-download the stuff you purchased. Also, it will delete the stuff you have on sysNAND if you go on the eShop through emuNAND after transfer.
I'm sorry if it's confusing. I'm really terrible at explaining stuff like this.