Illustrator :: Way To Make Background Transparent

I dont know if the t-shirt company will want the black layer and the white layer on seperate areas, so i will give them three files per side (black and white, Black, White).  Unfortunately when i split the colors in raster graphics and re trace them it doesnt do it the same! and i fear that their will be blank ugly spaces on the shirt.  so is their a way to take all of the white lines and put them by themselves on another document... and do the same with the black?
 
Also in the all colors toghether sample i have changed white to blue, so that it doesnt blend in with the background... Is their an easy way to make the background transparent, and then change blue to white?