Hi Kalle,
I've done a short write up about applying patterned fills. You can view it
here.
For applying a transparent pattern over the top I would copy that element and paste it on top and then apply the patterned fill. That way you'll have your original gradient and you can apply a transparent pattern over the top. There might be a nicer way to do that but that's how I do it.
For part 2 of your question it sounds like you're not filling the object with the pattern correctly. Select one of your brown patches and then choose the "pattern fill" option for the fill. It should only fill the area you've selected. If that doesn't work could you post an example of what you mean?