Actually, what you'll get is a nasty (usually) purple color covering a lot of the textures. JK uses palettes because all the textures are 256 colors. Each color is given a number 1 through 256, and each pixel of each texture calls for one of those colors by referencing the number. Thus, if you use textures from a different palette, it will call textures it doesn't want.
As far as JK's style of architecture (which is called "Negative Space Editing"), you have to think kind of backwards. The most important thing to understand is that sectors don't have outer walls. You can only see a sector wall from the inside. So, in the case of your building with the pillars, you want to cleave the pillars out of the sector, rather than adding other sectors overtop. Think of it like paper snowflakes. You cut out sections of paper to create the pattern, rather than adding more paper, or coloring the paper there. I highly reccomend that you read a couple tutorials
http://www.massassi.net/tutorials/outdoor/
http://www.massassi.net/tutorials/outdoor2/
These were incredibly helpful to me.
Also, kudos to you for trying something new. I think it's important to be able to understand where this site came from, and it saddens me that lots of people here now days don't know anything about JED or Negative Space Editing.
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