I normally use CS5 but I've recently started using creative cloud. My current version doesn't allow me to put less opaque shapes (let's say 20%) on top of the 100% opaque shapes, even when rasterize layers. When I tried to change the opacity, since it's not moving when I reorder the layers, it just sends them straight to the back even if they were on top before. It's really frustrating so any help is appreciated
You should be able to order all your layers except the background layer. Photoshop's background layer is a special optional layer on the bottom of the layer stack. It does not support transparency so it always canvas size a fully opaque.
I am struggling to understand your post.
If I understand you correctly you have some shape layers with varying opacity as I have shown below. The rectangle is 100% , The ellipse is 62% the polygon is 37%
If you use Layer -Arrange - to change the order (I reversed them) are you saying the opacity did not travel with the shape layer as it did below?