Don't use the smith machine as a guide when doing pistols (one legged squats) because:
#1) You are artificially interfering with the natural path your body wants to take in a squat position
#2) You are removing the balance aspect by leaning against the bar
Here's a pretty good example of a pistol http://www.youtube.com/watch?v=TWQnII4nt7M
(ignore the kettlebells). Focus on keeping the knee of the leg you are squatting on out and over your toes (don't let it fall inward). If you can't manage one at full depth just work up to it by not going ass to grass or by using a box (progressively lower).
Regarding your workout, in my view, as a novice (decent benchmark of novice in weight training is until you can barbell back squat 1.5X your bodyweight with good form) there is no point in doing a BB style split routine (upper/body splits). You will get more bang for your buck and spend less time in the gym doing a full body strength routine such as Mark Rippetoe's Starting Strength (buy the book from Amazon if you are interested, awesome information on strength training).
Workout A: Squat, benchpress, deadlift
Workout B: Squat, overhead press, power-clean (or bent-over row if you aren't comfortable with power-clean technique).
3 days a week, alternating (e.g. week one A-B-A, week 2 B-A-B). Each exercise is 3 sets of 5 reps other than deadlift is 1 set of 5 reps with the same working weight each time. You increase the weight 5lbs each day. If you cannot make all 3x5 reps you repeat the same weight the next time. If you fail 3 times in a row you deload the weight by ~20% and work back up 5lbs at a time. All exercises are done with a barbell/free weight (no smith), of course bench can be subbed for dumbbells if you do not have a spotter.
Doing a program like that you will have massive strength gains, observable goals/progress and not spend as much time in the gym doing a ton of exercises that are not really doing much for your body.
As for the bosu ball stuff, I personally don't believe it has any skill transference to skiing and I think it's dangerous for your ankles/knees. I did a bunch of it before last sesaon and did not feel it helped at all compared to strength training which made a huge difference.
Re: 90 degree knee squat thing, that is a myth. Your knees are in a more dangerous position if you stop at 90 degrees (which is not a parallel squat, parallel means the crease of your hip drops below your knees, not the angle of your leg) because you are producing a strong shearing force on the knee when you stop the weight, versus the natural position bottom position of a squat where the strong hips/hamstrings/glutes take the weight. The thing to be careful with your knees in any type of squat is that they are tracking over your toes properly and not caving inward. Also equally important in a barbell squat is making sure the weight stays over your midfoot/heels. If you get up on your toes (leaning forward) you will transfer the weight from your hips/posterior chain to your knees. This incorrect form is what causes the "squats below parallel are bad for your knees" thing. This is another reason why I believe smith machine squats are a bad idea, it's impossible to correctly position the weight over your midfoot/heels (midline stabilization).. I've been squatting ass to grass for about a year now and my knees feel stronger than ever.