Spider-Man: Homecoming mentions Peter’s room being across from Vision’s, so Vision hasn’t been missing the entire time since Civil War. The prelude comic acts as if Wanda met up with Vision immediately afterwards, but I don’t really trust those prelude comics.
Honestly we don’t have much to go on. I mean, presumably the rest of the Secret Avengers aren’t only staying in Edinburgh. They’re all close enough to come running when Wanda calls in the middle of a battle, so she must have been sticking with them.
So my gut leans towards Vision and Wanda meeting up on more clandestine interludes rather than being with Vision the whole time.
Including LEGO set spoilers and just about everything we know so far
The movie likely opens with Wanda and Vision staying together at this hotel in Edinburgh. After heading outside, they are attacked,
with the Mind Stone nearly successfully extracted from Vision,
leaving him injured.
But a timely rescue from Team Cap
allows them all to escape, and head back to the Avengers compound, with Vision still injured.
They meet up with Rhodey and Bruce and then head to Wakanda.
Shuri offers or agrees to help extract the Mind Stone (if the LEGO set is accurate) or help heal Vision.
Wanda and Vision stay with her as the rest battle Thanos’ army. It appears eventually things get dangerous enough that Wanda and Vision leave for the jungle, with Vision’s Stone still intact on his head, and Vision sitting on the ground, looking injured, and both know something is coming.
One last note, is that the Entertainment Weekly article mentions that Vision feels pain as the other Stones draw near–this could be inaccurate from them (because they do report some things wrong), but if so, it could mean that Vision was not damaged from the battle, but is reacting to the approaching Stones. Vision might be sensing them approaching, and that might be what Wanda is investigating here:
Wanda and Vision in Infinity War Trailer #2
Fandango Infinity War exclusive poster 2 of 5 (”Team Romance”)
Those Celestial Bodies 