Let me warn you in advance, that people in your position right now tend to find a lot of very different advice, and often get really frustrated. Try to be patient, keep learning, then chose a way to go. Try something for a while, the evaluate the results and change if you need to.
First of all, remember that BB.com is a specialized site for bodybuilders. We are a general-purpose exercise site with a variety of members. We include body builders, general health exercise people, strength trainers, strongman competitors, etc., etc. So is a way, this is a good place to come for advice, but also bad if you are hoping for a simple answer. There aren't any simple answers, here or anywhere.
The routine from BB.com is unwieldy for beginners, and looks to me more like it's intended for advance bodybuilders.
The main EXRX site has tons of good information, but I don't feel like it's the best and certainly not the easiest way to build a good routine. You can't possibly pick an exercise for every muscle--there are way, too many for this to even be possible. Instead of thinking of muscles or even muscle groups, think about movements. You need only one exercise for each major movement. These include 4 kinds of upper body and 2 kinds of lower body movements:
Vertical press (like military press)
Horizontal press (like bench press)
Vertical pull (like chinups)
Horizontal pull (like rows)
Knee-dominant legs (squat-like movements)
Hip-dominant legs and back (deadlift-related movements)
If you are afraid of deadlift because you are afraid of hurting your back, but on the other hand ask for an exercise to strengthen your back, you probably haven't thought about the fact that any exercise that can strengthen your back can hurt it. It is possible to learn to DL from the internet and youtube, but it would be better if you had a good trainer to teach you. There are other exercises that can be used in the place of DL.
I wrote a long post (not an unusual thing for me) on another thread about the characteristics of a good routine. Here
. Later in the same thread, Ironman (who considers himself primarily a bodybuilder, by the way) makes this statement: "I would recommend doing a very simple routine. Flat and incline press, rows, chins, squats, deadlifts. If you do that, you really can't go wrong." The only thing that would be different from what I'd say is that he suggests incline bench where I'd suggest military press.
So there you have it.
This is what I suggest:
Do two alternating workouts. One day do a squat (could be a lunge, step-up, etc), bench press and row. The next day do a deadlift (or other related exercise), chinups and either military press or incline bench. Start with easy weights, and do 3 sets of 5. Warm up for that with a set that's about half your working weight and one that's about 3/4 of the working weight. Keep the weights fairly light for the first few weeks, then gradually add a little weight each time. When you can't add weight and still do 3 sets of 5, check back for more ideas. Do them at least a day apart, but average 3 days a week.
About your knee, I don't know how a weak muscle can cause knee pain, at least not in such simple terms. There are weaknesses that can lead to improper tracking of of the patella. Did they give you a more technical-sounding name for your condition? What exercises did they recommend? If the source of your problems is weakness, then instead of shying away from exercises that put demands on the knee, you may need to start doing some.