Congrats on the new arrival!
If you refer to Wendler's 5-3-1, this is normally recommended as an intermediate program, and either a Starting Strength or Strong Lifts 5x5 is a good start and good to stick with until you exhausted the beginner gains. Usually it takes about a year, for men getting to 1.5 BW squat (for women about 1 BW squat) and most of lifts do not improve after a few deload-reload sequences once you get frustrated to keep coming back to stuck on weight). Then a Madcow or Wendler or any other intermediate program will take you further.
Yep, normally 2x a week associated with slower gains in men.