I have a couple suggestions:
1) For the squats, have you tried low bar squats? These may help the shear stress on your back compared to high bar squats. These have worked much better for me. If you go to youtube and watch Mark Rippetoe's Art of Manliness squat video, that might help.
2) I also do yoga regularly in addition to lifting and conditioning. As others have said, there are different types and you have to account for them differently in your training. If you're taking an advanced Vinyasa class, this is taxing on your body. I have noticed back pain if I add this to my weekly heavy squats/DL if I don't program it correctly. Then there is more gentle yoga and meditative yoga, that you can essentially do anytime and not worry about accounting for it in your lifting regimen.
3) Conditioning can be done on its own day, or fit in where you can. If you do hard conditioning - like hill sprints, timed 400m's, etc... - you need to consider how this affects your recovery and performance on your lifts. If you do easier conditioning - jogs, walks, weighted vest walks, airdyne, easier biking - you can put it in where it fits and not worry about how it affects recovery and lifting performance.