I tend to put the more difficult skills towards the beginning of the workout, especially with balance stuff. I don't like to be overly fatigued and trying to do handstands or pistol squats, as my technique goes to hell. Do a warm-up, then do your skills, then strength.
Unless of course, building strength is more important than those skills, in which case do the strength training first.
Another option for skills is a grease-the-groove approach, where you do small sets of a skill throughout the day- just a few reps, or a few seconds of a hold. Don't ever go to failure, but do these frequently. This shouldn't affect any of your other workouts significantly. If they do, back off on them.