Use layer masks!
Basically a layer mask is a sub-layer to one of your layers, which controls the opacity of every single pixel. White on the layer mask means full opacity on the real layer, black means full transparency. grey means 50% transparent, and a lighter grey gives you a bit more opacity. It sounds complicated but basically you paint on the layer mask with different greys and the darker the grey is, the more transparent the layer becomes on that part.
To create a layer mask, rightclick on your layer in the layers dialog and choose "Add layer mask". Once you clicked on the small preview image next to the layer preview image you can paint on the layer mask.
I'm so bad at explaining things