I have only just started simplefit, only on week 3 but I am also adding more cardio and running on my SF off days. Though I don't have much experience, can I suggest following a squat progression series? If full squats are easy and for each level you progress you can complete the required number without difficulty, maybe work your way to pistol squats or do an intermediate step between pistol squats and regular full squats, such as assisted one leg squats. http://www.youtube.com/watch?v=TWvIu7s-vIM
Hope that helps, I know there is a lot more information out there on how to combine bodyweight routines and cardio effectively too, I just haven't gotten there yet =). Still only doing about 10km of running a week.
Edit: Meant to say adding pistol squats/alternatives on days that don't interfere with your recovery after especially difficult runs.
Double Edit: I feel like I didn't add anything as to why progressing up to more difficult squats may be helpful, other than the assumption that being more difficult will make them not feel pointless. Not the most academic source, but has a lot of good information about the role of strength training and how bodyweight squats can be part of that. http://www.runningtechniquetips.com/201 ... technique/
Which comes back to the point that if full squats not helping develop strength, maybe time to try more difficult bodyweight squats.
Hope there is something useful in all that, though, everyone has their own way of exercise that is optimal to themselves. Find what works best for you!