I use iRealpro as my backing tracks. I will use the last 30-60 minutes of my daily practice to shed whatever I've been working on in the context of actual tunes. So if I've been shedding some new vocabulary (without backing tracks) I will go through a few tunes trying to incorporate the new vocabulary into my improvisation. Or if I've been working on, say, diminished scales, I will try to incorporate them. Or intervals, pentatonics, substitute chords, whatever. I keep the lead sheet (usually one of the Real Books) in front of me, and I also find that doing this helps me to memorize the heads and changes over time and to get the changes into my ear. Then for the last couple of tunes for the day I'll usually just play to see where I am and try some stuff I might not want to risk doing live until it's more comfortable.
That said, when I'm first learning a tune I will not use backing tracks, although I will probably listen to a recording of the tune to get a feel for it. I'll go through the changes arpeggiating each chord and inversions top to bottom and bottom to top, then play all the roots through the tune, 3rds, 5ths, etc. Once I get that down, I may repeat this process using the backing track just to hear how it all fits together. Then I'll use the tracks to do what I described above.
I go through the real books (I use volumes 1 - 3) front to back over time to make sure I play lot of different styles and keys and don't bias myself to certain tunes or styles. Once I get to the end of the three books I'll start over. I also add in tunes that my bands might be doing that aren't in the real books (I like that I can add tunes to iRealPro).
One other thing that comes to mind is that we occasionally play tunes in odd meters (e.g., we like to do Speak No Evil in 7) and I'll edit the time signature in IRealPro and crank up the backing track to get used to the new meter before embarrassing myself in public. Actually it's a great way to get used to odd meters, if that's something you want to work on. Take any tune you are familiar with and change the time signature.
Oh, and we have a vocalist who almost never sings in the real book key, so it's a way to shed playing the tunes in different keys.