From my limited knowledge of the workflow, I’d suggest doing the boxes in Photoshop and bringing the layers into AE as a comp and working on them there. It’ll offer a lot more flexibility, and I suspect, ease of processing/rendering.
There are a number of tutorials and how-tos with respect to formatting for diff resolutions on the Cow, which you can search for. Alternatively, there is a good tutorial on toolfarm that explains formatting stuff for NTSC TV, and I think the same woul dapply for this format as well.
I am an AE newbie, and apologise if I couldnt give you a more substantial answer, but i wasnt 100% clear about what you were trying to achieve so I could point you in a more precise direction.
DVV