Question about when to do cardio...

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Okay, I am 24, 5'4" and about 118lbs. I have been eating "clean" for a few months now while doing P90X. For a while I was also doing an hour of intense cardio every morning before breakfast but after reading some threads on here I decided to focus more on the weight training and just do a few shorter cardio sessions (including some HIIT) a few times a week instead of an hour a day. I don't feel like I need to lose a lot of weight... maybe 10 pounds... I mostly just want to exchange fat for muscle. When I was doing my cardio in the morning I did it before breakfast and I feel like maybe I was burning through some lean muscle instead of burning fat... so my question now is, if I decide to do a long cardio session (go for an hour run or something) should I do it in the afternoon after I've eaten a few meals and have some calories to burn? Or does it not really matter... I just want to make sure I'm building muscle, not burning it. Thanks!

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