Yes, I think they know which catchers handle pitchers better, and which pitchers it doesn't seem to matter as much who catches them.
My guess is, some pitchers do voice a preference, especially if they keep getting paired with a catcher they don't seem to be in sinc with as easily as they feel they do with the second catcher.
It's obvious some pitchers are given just one catcher almost exclusively, and it's almost always the one known for defense or CERA-related intangibles.
I'm guessing one reason we traded for McGuire, is that they think he's good with the staff. I'm not sure how they view Wong. There was a lot of talk, when we got him, that he may not stick at the catcher position. Soxprospects.com writes this about him, "Moves well behind the plate, and has improved his receiving and framing skills to the point where he is considered solid with both... Has been able to develop a good rapport with pitchers and become someone they like throwing to and have confidence in. Potential solid-average defender."
If they view both catchers somewhat equally on defense, then maybe they can start the season with a platoon, and see if certain pitchers and catchers work better together. They did not have much time with the staff, last season, and most of our starters are gone or were on the IL to end last season, anyway.
Here are some tiny sample sizes- hardly worth mentioning at all:
CERA
Bello
8.82 w Vaz (16.1 IP)
3.20 w Wong (25.1)
2.87 w McGuire (15.2)
Whitlock '22
7.20 McGuire (5 IP)
3.42 Vaz (52.2)
2.89 Plawecki (18.2)
0.00 Wong (2.0)
Pivetta
OPS Against
Bello
.592 w McGuire (67)
.775 w Wong (118)
1.027 w Vaz (83)
n/a w Plawecki
Whitlock
1.000 w McGuire (21)
.670 w Vaz (215)
.473 w Plawecki (68)
.143 2 Wong (7)
Pivetta
.907 Plawecki (73)
.840 w McQuire (186)
.754 w Wong (58)
.692 w Vaz (456)