I installed a rectangular liner last year, and I had to rework it a bit to get the side seams even all the way around and all of the corners in the corner.

I used the vacuum method to get out most of the air out from behind the liner, then did a shallow water fill. I did have to drain the pool down to even out the side seams so they were plus or minus one inch.

After I got the liner in the final position and all the floor wrinkles out of the bottom, I filled to about 6 inches and cut in the lower side wall drain. I then filled the pool and adjusted the liner and coping connections as needed (off by a bit in the corners). The last thing I did when everything was straight was to cut in the upper return connector and skimmer.

Is your skimmer and return outlet cut into the liner yet?

Anyhow, I would probably drain and rework the liner a bit if at all possible to get the sidewall seams close to even (but not perfect).