I created a clean UNEEK NAND with ModMii, then launched it with neek2o, configured the nand settings like wifi synced remotes, setup screen resolution etc. Then I named the folder "flownand" and put it on the root of my USB, afterwards I set the path in the .ini as /flownand/ and it returns to loader when I quit with Wii Menu. I'm using d2x v8 final 245-251 with bases recommended by wiiflowiki.
I don't know the technicalities of how it works but I'll post a vid cuz its crazy, it's been said that for a long time they don't work due to how they're compressed but I assure you they're working for me.
Edit: Well I stand corrected. Sin & Punishment and LOZ: Ocarina of Time Masters Quest (Injected VC) were the N64 games I was launching with WiiFlow+. I just attempted to launch LOZ: Majora's Mask and it hung on a black screen after the spinning "N" logo for N64. My apologies, as some N64 VC launches but Majora's Mask does not.
Majora's Mask does launch under my neek2o setup so I know it's not a bad WAD. I'm still going to post a Vid of Wiiflow+ launching other N64 titles if it helps.