On my touring bike, which I built up myself a couple of years ago, I have
brake cables with an outer-inner or inner-outer like you describe. Looking at the packet on
Wiggle for Black Snake cables, it's familiar to me, so I think this may well be the brand I fitted.
I left inner cable liner on for the whole cable length and they're good after lots of tough use. I don't recall having your quandary though so I've no idea why I decided to fit them the way I did, but if I had instructions, I'd probably have followed them.
Not sure if that's any help!