2) The Compressonator reported fatal error. Even try Gimp.
For the compressonator, maybe you have use the 64bit version on a 32bit version... well, you first problem seem to be the alpha channel... before you try to made the final conversion to .dds, in what format do you save your work? If it is .jpg, alpha channel will be discarted... use .png ... best, use .tga who use a loosless compression...
Will help if you post your files...
3) No. I ask how to put the edited file, for example FrigatePsiLight.entity, to the mode.
Entity File need to go in "/Documents and Settings/Administrator/Local Settings/Application Data/Ironclad Games/Sins of a Solar Empire/Mods-Entrenchment v1.053/g4_test/GameInfo"...
well, it is true only if your mod is for Entrenchment... and if your mod is called "g4_test"...
http://soase.weebly.com/placing-mods.html