There are videos on youtube of how to setup layeredFS for NTR. I believe @DarkFlare69 has a few youtube videos that go over how to set up and use different parts of NTR, including one on layeredFS. As for compiling a custom CIA of it, I don't know how to do that.please...how? i'm noob on this
But to do either of those, you need CFW, which I assume you have based on the fact that you said you were using the HBLauncher_loader cia to load HBL.