Do your conditioning after your work out or on days when you're not training at all. Do not run. Or, don't do long slow distance. If you want a LP program with wisely conditioned breaks in it,
this is the program you should be doing till you get strong enough to switch to the
Grayskull LP Linebacker Template. You can, literally, change into the other program next week without tweaking any lifts.
If you have a hankering for conditioning, do 10-15 minute intense metabolic conditioning sets. Barbell complexes, some of the smarter designed Crossfit circuits, anything from the Grayskull conditioning books (all of which are fucking brutal and perfect for people looking to work up a sweat), prowler work, etc. Long distance running will put your body in a state to make you more apt to do long slow running, I.E. lighter and leaner, but in the wrong direction for muscle strength/size building.
Think about the way Usain Bolt looks versus any marathon runner.
QUICK EDIT: You can continue to do SS, just be warned it's very brutal on the body with squatting 3X per week and is designed around NOT running. It's more than just recuperating, it's injury prevention, progression, program swapping in the future, etc. If you want to run, run. Just understand that, at that point, you're NOT doing the program.