Igloo Proof and other Nikwax products only serve to re-wateproof, or repair waterproofing on fabrics that were already waterproof to begin with. You cannot apply any Nikwax products to just say, a cotton, and then expect it to work as a cover. It won't. What it does do is repair small cracks and holes in PUL or waterproofed nylon so that covers or AIOS stop leaking.
I've never had to use Nikwax products on fleece covers or AIOS, it's the actual polyester fiber and how it is knit that makes fleece work as a cover or barrier fabric. DWR or "durable water resistant" coatings wash out - I've never understood the obsession with them, the fleece will still work without it. However, many insist that fleece (or PUL) without DWR don't work as well (I disagree) so the Nikwax products will put it back in. It will wash out with continued use though. Nikwax products were developed for outer ski wear, items that aren't washed every few days like diaper items are.
What I have seen work well is Nikwax seems to "help" when an outer print AIO is leaking at the legs. But still - I'd just omit the outer print.
HTH!