Paint.NET :: How To Add Effect To Multiple Gradients Properly

I'm making userbars, and I'm using the trick to have multiple gradients in multiple layers. (I don't really think I'm doing it right though, first I make the whole first layer a certain colour, then go from the left with the next colour with the second colour transparent?) And for those layers, I'm trying to add the cloud effect (something to make it look nicer, I hate how lame/2d it looks without any effects) to all the layers with them blending into each other, but I eventually see one of the clouds effects under another effect/colour and it's just a big mess- I can see every colour mashed together. When I use the rectangle tool to select where the cloud effect goes, or the eraser to erase what I don't want, it looks kinda square like, and it doesn't blend with the other colour. ;-;

I have the plugins all downloaded btw.