The file from episode 1 to transfer to episode 2 only fits the one you made in the basement of Monica's house (at the end of episode 1). At that point, the game
will prompt you to save so that you can then continue playing episode 2 from that save. See
FAQ (1.1.5). In most cases, this scheme works. However, sometimes you might encounter a problem when your save file from Ep 1 is not accepted by Ep2. That's where you did the right thing - answering the questions at the beginning of Ep2 v16 (New Game) allows you to avoid these problems and continue playing with a working in-game quest log and all the choices your Monica made in Episode 1.