Sounds like you pretty much understand it! You can still put a layer of fleece next to dc's skin if you want: a fleece liner, a fleece-topped doubler, or a fleece-lined diaper. If you don't, then, yes, the wetness will be against the skin, as it would with any diaper-cover combo that doesn't put fleece against the skin.
What you'll find most different about a wool soaker, I think, is that it's breathable, so--especially during warm weather--baby's bum stays cooler. I can notice a big difference. Sometimes when dd is wearing a Bummis cover & sweating, I'm not sure if her dipe feels damp from having peed a bit or just from sweat! With a wool cover, she's not sweating inside the diaper, and if I don't change pretty quick after she pees, the wet dipe actually starts to cool off!
For now, while the weather's warm, we use wool as an outer layer only. If you're going to put clothing over the soaker, be sure the diaper underneath is good & absorbent & the clothes aren't too snug, or you may have compression wicking onto your dc's pants.
HTH! Hope you enjoy knitting your soaker--I've loved making mine & seeing dd in them!