The Elder Scrolls XVI: Sworn to Carry Your Burdens

[Aeson]

Arent most of them inside the Ghostfence?

None of the eleven Dunmer strongholds are within the Ghostfence, and I think only Falasmaryon, Telasero, and Kogoruhn have a clear Sixth House connection in Morrowind. You might be thinking of the Sixth House Citadels, where the Ash Vampires can be found.

There's definitely one that tunnels under it.

That'd be Kogoruhn, and Kogoruhn itself is outside of the Ghostfence, in the northern Ashlands near the Urshilaku Camp.

Kogoruhn is also unique in not having a functional Propylon Chamber.

And I can't remember where Redoran's was. Somewhere by Ald-Ruhn?

Indarys Manor is at Bal Isra - if you take the road from Ald'Ruhn to Maar Gan, it's roughly midway in between. A bit more out of the way than Rethan Manor at the Odai Plateau, but not nearly as isolated as Tel Uvirith is at Uvirith's Grave.