Punching in was needed with analog tape recorders. There's no need to do that now with DAW software. I use SONAR, so when I'm ready to lay down a guitar or bass track I define a looped section from one bar before to one bar after the part I'll play. Then I hit record, and play those bars over and over until I'm happy. Then I pick the best take, or edit several parts into a single take. This is infinitely easier that punching in.
--Ethan