Layer 2 Editing
Wrote by: FullOfFail, redistrubute as nessasary.
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First and foremost, make a backup of your hack. If you click the wrong thing on the pointers tab, it'll over-write data. 

For Non-Sky-Scrolling Rooms:

Step 1

Edit > Pointers 
Change the BG_Data pointer to 0000
Press Save Pointers and Click "No"

Step 2

Tools > Background Editor > Add Later 2 Background
Press F1 on the keyboard to alternate between layers (or View > Layer 1/Layer 2)
Clean all the yellow doors on Layer 2. 
(Fastest way to do this is select and empty tile from layer 1, then go to Layer 2 and click Edit > Special > Fill Area.)

Step 3

Tools > Background Editor > BG Layer2/SCROLLING
Change the top box to Layer 2 Background (custom)
The Y and X coordinates are how much the Background Scrolls. Y=0, X=0, will make the background stationary. Otherwise, just experiment and find what works best for you. 

Save. 

That's it. All you have to do now is create the BG.

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For Sky-Scrolling Rooms:

This one is a bit more tricky, but I'll try to keep it simple. I'll be using the landing site in this example.

Step 1

Go to a room that doesn't have a Sky-Scrolling Background. The second room on this list should work fine. But for this example, I'm going to use 7B051, because it's a fairly useless room. 

Go to Edit > Pointers and highlight the Layer1_2 value, and Right-click and select Copy (Ctrl+C).

Step 2

Go back to the original room with the Scrolling Sky. 

Go to Edit > Pointers and highlight the Layer1_2 value, and Right-click and select Paste (Ctrl+V).

While in the pointers tab, change the BG_Data to 0000, and the FX2 to 0000 aswell.

Press Save Pointers, and Click "No"

Repeat Step 2 for every State (The menu beside the Room Number.)

 Step 3

Tools > Background Editor > Remove Later 2 Background
Tools > Background Editor > Add Later 2 Background
Press F1 on the keyboard to alternate between layers (or View > Layer 1/Layer 2)
Clean all the yellow doors on Layer 2. 
(Fastest way to do this is select and empty tile from layer 1, then go to Layer 2 and click Edit > Special > Fill Area.)

Save Room.

Step 4

Tools > Background Editor > BG Layer2/SCROLLING
Change the top box to Layer 2 Background (custom)
The Y and X coordinates are how much the Background Scrolls. Y=0, X=0, will make the background stationary. Otherwise, just experiment and find what works best for you. 
Repeat Step 4 for Every State (The menu beside the Room Number.)

Make sure to Save to room after you changed it for each state.

That's pretty much it. Should be all set now. But note: When you changed the FX2 Pointer, it had the side-effect of also removing the Escape sequence (listed as the State: Events 1)  routines (Such as the random explosions).

To fix this, go to the room 792FD, then go to the State: Events 1, and copy the FX2 pointer. Then go back to your original room and paste it in the pointers tab for FX2, the State should be: Events 1.

Also, even though it should still be perfectly usable, I'd just not use the room we stole the Layer 1_2 pointer from (room 7B051 was what I suggested). From what I've tested, it seems to work fine, but I'm not entirely sure what the Layer1_2 pointer does exactly, so it could end up glitching out. If you chose to use it, make sure to thorougly test it.

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I know this all seems like alot to take in, but after doing it a few times, it becomes a second-nature.