It can be tough to get started when you're in pain, but as you learned, it's worth it! Once you start moving and feel the benefits, you won't want to go back.
Some days the pain in your joints may be worse than others. When that happens to me, I modify my routine for a few days. Rather than run, maybe I'll walk on an incline. Rather than doing my scheduled lower-body weighlifting routine, I'll do upper-body. Switching my cardio to swimming on days when my knees hurt is always mty best option. I'm never sorry about that decision.
Spinning is a class you can take at the gym during which you ride a stationary bike. The instructor takes you through a workout in which you increase and decrease the tension on the bike, stand up while riding, sit. Loud music.
When my knees are bothering me, I have trouble with lunges as well. Not sure if you belong to a gym, but if you do, you can try leg extensions or leg presses for quadriceps strength. I'm sure you could rig up something at home with exercise bands to simulate the leg extension movement. http://www.workoutz.com/exercise/leg_extensions_with_exercise_bands
Mind you, I'm not a fitness expert. These are just examples of what I've done for myself.
Arthritis Today has some others to try: http://www.arthritis.org/media/FIT%20Sitting%20exercises%20web(2).pdf
To understand the exercise process better, I recommend reading "Younger Next Year". Good luck. Alan