You are better off not using the Smith machine at all. It forces a very strange bar path in the squat. Start off using a bar only or DB at your sides, hell anything but a Smith Machine.
Yep, squatting 2x/week is better than once, especially if you want to get anywhere with it.
Your numbers are decent for those BW exercises. Most of the pull or pushup programs generally deal with just doing more volume.
So it's either that or get beast enough strong that a BW exercise is so easy that you can do ridiculous reps. This will take a long time.