I majored in history in college and I have done a lot of independent reading on the history of the Civil War but I only just thought about tackling this question in depth and I hoped that the org might have some ideas.
During the American Civil War what percentage of confederate soldiers owned slaves?

Obviously only a small percentage of the Confederate Army would have owned slaves, as most confederate soldiers were small-scale farmers or local artisans and neither needed nor could afford to own slaves. Most of these small producers in local ecnomies would rent out slaves from larger farms or plantations during the harvest or planting seasons, so they used but did not own the slaves. I am guessing that less than 10% of confederate soldiers owned slaves and that only about 1-2% owned more than 50 slaves. Prosperous middle-class farmers, tradesmen, and merchants might own one or two slaves as domestic help or as field hands, but the vast majority of slave owning was confined to large-scale slave holders who used them both as workers and investment properties.

I have seen some figures that try to give the percentage but they don't list sources and they are often published by Confederate Remembrance groups or Confederate flag supporters, and they present the statistics in the context that "the south wasn't that bad".