Editing Textures-slight problem

[NEXUS]

Hello, I have edited some of the textures and they look fine in the game, but if it is a texture that uses a transprancy colour, when I edit it I see black and or white boxes around the cursors, cyborgs, and anything else that has 'see-through' bits in it. any help as to what colour I need to use for editing these coulors for frontend textures (used to be a navy blue colour) and regular textures (used to be a neon-green colour)? as the regular colours used from the base.wz file do not seem to work for me.