Ai offers you either RGB or CMYK; you decide which in the File > Document Color Mode ( circa v10 ). Transparency doesn't care which space you use in Ai. If you work in CMYK, then just make sure your swatches and images are CMYK. But, I think there are other reasons why you'd get boxes in transparent objects. Take a look at Flattening.
Thanks. That gets me the information I need.