I wouldn't feel bad or awkward at all about talking to the guy who fit you. The whole entire point of his job is to keep you from having pain, assuming it's the fit that's causing the pain. Maybe the way he fit you works for some people, but not for you. I would be surprised if he charged you more money.

I would give him another shot, assuming he doesn't charge you anything to adjust the bike. If that doesn't work, try another fitter.

Where is your knee pain? When I was trying a new saddle a while back, my husband put it on for me. A couple of rides later I realized I was having pain behind my knee. I finally figured out it must be from the saddle height. My previous saddle had been set by a professional fitter. Anyway, dh raised the saddle, thinking that was the issue. The pain didn't go away, so I took it to my fitter. He said the saddle was way too high. He said that "typically" pain below the knee means the saddle is too high. Pain above the knee means it's too low. I didn't have knee pain after he adjusted it.

The right fit can mean everything and, like I said, I'd be surprised if he charged you more to adjust it and if he wasn't even upset at all that you asked him about it. I would think he would want to know if you are having any problems. I know my guy would. My guy did make it clear to let him know if I needed any adjustments. He also made a point that a previous poster said, about changing things in small increments. What works for you now, might need even more adjusting in the future.