Too little time...
It's tough to fit everything in! I bought those Windsor pilates videos from the infomercial and I never have time to do them. They claim to tone your entire body...yeah right. For me, the pilates tapes weren't time effective. I could feel my abs working, but the video was too long-I'd rather do a tough, fast ab-specific tape. That's just my opinion.
Yoga is great though after a tough workout. I do 15-20mins of yoga after runs or spinning. It's good to stretch and relax. Your body feels melted afterwards- a nice feeling.
As for toning, I don't think pilates or yoga (unless you're doing advanced yoga) are considered weight workouts. They're more for stretching/relaxation, and toning is a secondary benefit.
I count kickboxing, spinning, running, etc as cardio- toning your legs, abs and/or arms are secondary benefits. It's not really weight work though. If you're sore, I'd just skip the weights for that day.
My advice is to find time-effective workouts that you like. It may take time to realize that you might get better benefits if you tried a different workout, video, etc. Some CIA videos have toning and/or yoga after the cardio, which I love since you get it done.
You could make a chart and write your goals: maybe 4 cardios, 2 weight days, and 2 stretch days and try to complete it all by the end of the week.
Good luck!