There are super ancient pics of Yes/Squire from The Yes Album (and before) where Squire has Fender Showman amps with 2x15 cabs and other stuff but ...
In the classic 70's prog Yes period from around Fragile through Going For The One, Squire used 2 Sunn 6x12 cabs - that's right, 6x12 (not 6x10). They were tall and fairly wide and somewhat unusual.
For amps, he used an early 70's Sunn Coliseum Lead head (solid state) for Fragile, Close To The Edge, Tales From Topgraphic Oceans, Relayer and beyond.
He also added a Marshall 100W Superbass for his distorted sound starting with Tales From Topographic Oceans sides 2-4 and for a lot of Relayer (Sound Chaser and Gates Of Delerium) and beyond. He usually had the Marshall head right on top of the Sunn which was on top of one of his Sunn 6x12 cabs.
I don't know how (or if) he switched between the amps or if each had one Sunn 6x12 cab or what.
He ran his pickups stereo but I don't know if he ran them through separate amps. I think he ran them through separate channels (each with its own eq setting) on the Sunn, which is a 2 channel amp. How the marshall played in, I don't know either but you could certainly hear it on songs like Ritual and Sound Chaser. That was the tube Marshall. It was a very different (and awesome) sound. He used that distorted Marshall sound a lot on his solo album, Fish Out Of Water, from that same (Relayer) period.
On the Yessongs movie he has the solid state Sunn Coliseum and the two Sunn 6x 12 cabs. That was the Close To The Edge tour and before he added the marshall.
Starting with the Tales tour, he had the same rig but with the Marshall head also, for his distorted sound.
I saw Yes live 5 times on separate tours over around 5 or so years back then (starting with Tales) and he had that same rig every time for at least 4 of them. The last time I saw Yes was "in the round" on the Tormato tour and his amp wasn't visible.
He had 2 distinct and very different sounds then:
The relatively clean and trebly Fragile/CloseToTheEdge/TalesSide1 sound
and the less trebly and quite distorted TalesSides2-4/Relayer... sound. He also alternated these 2 basic sounds on songs on both Going For The One and Tormato.
There is an old 1973 Squire interview from Guitar Player magazine (also reprinted in a book called Bass Heroes) where Squire gives his exact amp settings (on the Sunn) but it won't do you much good because that was on an old amp that you don't have.
Different amps are voiced differently, so I hate to be vague but you will have to use your ear.
One thing for sure, Squire has a very hard and agressive attack and he is not afraid to let those strings buzz. Listen to Close To The Edge, he's hitting hard and in a certain way to accentuate that bouncy grind sound. You will have to experiment. He also used brand new, bright roundwound strings, of course. Back in those days it was Rotosound Swing Bass for both he and Geddy.
I was a big Squire fan back in HS, ha ha, bet you can't tell.
You've definitely got the right bass - but do you have the right speaker cabs? Back in the 70's, Chris Squier used Sunn amps with 2 double-15 boxes. No doubt, his setup changed over time.
I just recently saw Yes on a TV special, but I couldn't tell what he was playing through. I can tell you that the bass and the speakers are going to change the sound more than the amplifier will.
