Backgrounds
Backgrounds are extremely important when designing a mission. In addition to breaking up the constant blackness of space, backgrounds set the mood for the mission. If you are creating a standalone (non-campaign) mission, you can use whatever colors you like, regardless the colors don't clash. If the mission takes place in a system featured in the single-player campaign, it is ok to base your nebula backgrounds based on that particular mission.
If you are creating a campaign, be sure to create templates before starting work on ANY missions. It would also be a good idea to write down the number of planets, the bitmap associated with them along with their orbit. This will come in handy if you have a mission taking place closer to the star, and therefore the closer planets will be larger or only be seen. Make each system unique to give the player more than just the same color backgrounds over different systems. Some ways to vary systems include different numbers, colors and sizes for suns; different nebula patterns and planet systems.
Whatever you do, make sure to create your backgrounds first so you won't have to worry about getting killed while admiring your nebular handiwork.
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Nebula background
You can create very nice nebula background if you are using many, low-scaled images. The optimal scaling factors are between 2 and 4, but you may choose to use larger scaling factors for more detailed (512x512, 1024x1024) images.
You will also have to be familiar with how FRED handles the co-ordinates for the background images. You should move between the horizintal values of 60-280 approximately to get the nebula piece to the co-ordinates you typed in. Becoming familiar with the FRED background co-ordinate system requires experience. You can also use bank(rotation in another word), or pitch (for changing the height).
Using extreme-scaled ({6,6} or higher) nebula textures is simpler, covers more space, but produces blurry results. If you want to use large scaling factors, try using the large scaling for only one axis, and using a small factor on the another axis. (Examples: {5,2} and {6,1})
Mix RED with GREY, or BLUE with GREEN to achieve optimal nebula colour results. According to my experience, mixed nebulas of the colours RED and BLUE are somewhat ugly. But this is my opinion.
One should add planets to your backgrounds only after you are satisfied with your nebula background. The reason for this is simple: the game renders the background textures according to their place in the background bitmaps queue in FRED. Therefore, the first element in the queue will be painted first, the second will be painted second and so on. In addition to this, the later elements in the queue may be placed in the foreground compared to previous elements. Thus, if you have a planet first then a nebula, you may have the planet appearing behind the nebula, instead of the nebula appearing behind the planet. Afterall, the nebulas are supposed to be many lightyears away.
There are three main ways to create backrounds for missions you create in FRED:
Creating backgrounds from scratch
Wether you are using flashy custom nebulas or the stock nebulas, placing nebulas is rather hit-or-miss. For each background bitmap, you must line up the nebulas using the pitch/heading/bank edit boxes. After each significant change, you must test the mission to make sure your tweaks have worked to your desire. You must also make sure each nebula bitmap isn't too streched to make it distorted. Keeping the bitmap's scale values nearly equal will avoid this. Additionally, bitmaps that have really large scales look too streched even when the scale values are nearly square. As with any other topic in FRED, you will get good at this once you have experience.
Using a background generation program
A few background generation programs can be downloaded that will randomly place background bitmaps for you. After running the program, it would spit out a mission file that contains the background. Some tweaks are necessary to get a realistic background, since you may need to change the background's bitmp, pitch, bank and/or heading. This method is much faster than creating backgrounds from scratch. Documentation for each generator varies and it would be a good idea to read it before using.
Skyboxes
A recent addition to the Source code project, skyboxes allow users to create a skybox model and place it around the field of play much like the background bitmaps. They are rendered in addition to the background nebulas, so be sure to include either a skybox or nebula bitmaps, but not both. To create a skybox, read the Skybox Option page.