Messed textures in a model

Ok i am new to modeling .. However i have experience with 3dsmax so its not so hard.,,, but there is one problem. In 3dsmax the textures are always messed (probably because i use indexed color from photoshop for the textures) .. Lets say ive got a ninja character and ripped texture of the face,body etc. with a black background.. The problem is when i apply them the model always turns black and nothing can fix it .. not UVW Map nor Unwrap UVW.. Even if i manage to get it "right" in some kind of weird and sick way when i compile the QC file in milkshape and when i look at the final result the textures are always messed around ..So what is the proper method to apply the textures in 3dsmax so they are fine in the final result .