Not sure what you want.
In the past it was useful to install Lain first and while installing do not install the bedroom file.
BUT, you will get problems with it. So everytime you enter Aunt Dianes Shed, the time change to evening. You get error messages during scenes with Jenny, but they don't stop the game. There are maybe more issues.
I would use only one of them. Lain or Naughty.
Both are good. But even if Lain's Walkthrough is very good and I really like it, I prefer Naughty in the moment, because the Wiki and the phone hint app in the game are enough help to play it. The extra scenes from the lains mod do not really fit to the characters in the moment, in my opinion and the quality is not really good.