Lumbar pain on sitting. Knee be related.

I am having lumbar back pain which increases after sitting for long hours in office since last 2 years. Pain is not consistent and will be there for some months and will not be there for some months. Pain is not there in the morning but as the day passes pain increases. I have performed exercises as per physiotherapy classes. MRI only says Subtle posterior disc bulge effacing anterior epidural fat at L5-S1 level. Mild posterior disc bulge indenting the thecal sac at L4-L5 level. HLA B27 is neagtive. Though pain is not affecting my daily activities and pain is manageable but I was actively involved in sports which i have stopped now. Need to understand what can be the correct course of treatment to first get rid of pain and then gradually resume sports/injury. Also I have developed knee pain some months ago and my doctor has diagnosed it as chondromalacia patella. Can this back pain and knee be related.