Yeah he had very little to do with it, and he's on record as hating it. I think he only directed the first and last episodes, the finale was pretty good.
He directed four episodes of Season 2. The first, the second, the seventh, and the last.
On the first season he directed two episodes: the pilot and episode 3 (or 2 depending on how you count). Soon after filming episode 3 (or 2) he went on to film Wild at Heart.
He was very much around during the first 1/3 or half of the second season but, while still being around there in the office etc, he did distance himself from the production during the second half of season 2. He still chimed in to give notes and ideas though (the desk knob thing was his idea and at one point near the end he gave a note that Windom Earle should wear black all the time).
There is this rumor that Lynch left to make Wild at Heart during season 2 and that would be part of the reason why there were problems with that season, but the timeline doesn't add up. Wild at Heart was completed before season 2 started.
Reflections: An Oral History of Twin Peaks is a good book to read. In that book Al Strobel recalls how they were filming the scene where he is found at the motel (episode 4 - or 5 depending on if you count the pilot) the executives were in the set and tried to stop them from showing his amputated arm so they called to David as he was filming Wild at Heart and David told them on the phone that the amputated arm will not be covered.
Now, they had written or at least outlined the whole first season before they started to film the episodes beyond the pilot and David was around all that writing part, but he went away somewhere before half of the season was filmed, and after the season was completed he was still filming or post-producing Wild at Heart. So while they were writing and outlining the second season he wasn't that much there with Mark Frost during that writing process, but as they started to shoot the second season episodes David was already back and he directed the first two episodes and he was able to be around full time again.