So I've drawn a design in Illustrator CC that has some transparency throughout the actual shapes (not just the background). When I save the file as a .eps and open in photoshop, the background remains transparent, but the shapes themselves are completely opaque again. How can I maintain the transparency when saving as a .eps from illustrator?
That would be because EPS is not a authoring format but rasterization instructions. It has no features to support transparency, layers etc that could be read back from the system.
(this is not because eps could not and does not have the ability to have transparency its just a interpretation issue)
Just open the AI file in Photoshop.
Save the file in EPS10 format - it supports the transparency.