Can I select something across multiple layers?

[Geocide]

Hello, I am making a heightmap for the game Teardown, and I am new to complex editors like gimp entirely. 

The port (the section with uniform color) and the ground above the port, shown as a brighter red, are on different layers. I need to select the area within the port, minus the area covered by lighter shades of red. If it's helpful, the reason I need to select this particular section is because I want to add a specific shade of blue on top of this section on a new layer.
The preview isn't showing the image, so in case it doesn't work, I will also link the image below. Thanks for any help!

[Ofnuts]

The selection mask (what everyone abusively calls the "selection") applies to the whole image, not to a specific layer. But it can be created/altred using data from one or more layers. In your case:

• Select (as in "making current") the port layer, and create a selection from it (say, fuzzy select)
  
• Select the ground layer, set the fuzzy select tool to Subtract mode (top row of red icons at the top of the tool options) and make a selection on it. This selection will be subtracted from the selection obtained in the previous step.
  

There are other tricks to know, see: Painless use of selection tools

[rich2005]

@ Geocide

You have set up nicely What you can do is
Go to the port layer then Layer -> Transparency -> Alpha-to-Selection. That will select all the red block
Go to the above port layer then Layer -> Transparency -> Subtract from Selection. Using that will keep any semi-transparency in the selection.

You can check the effect with a fill: 30 second demo: https://i.imgur.com/iZlsUbM.mp4

[Geocide]

Thank you! Both of these suggestions worked