If I attach the marquee to the plywood will it hurt the final look?

[upper2bits]

I was planning on just attaching the marquee to the top and bottom parts of the wood(see photoshoped picture) but I'm worried that since no light will shine through the edges it might look odd.

[bgmagic]

It will be fine.  All my arcade machine marquees have been setup like this.  The center is the important part.  You won't notice that the very top and bottom arent backlit.

[syph007]

Ya I did that to my big build and it did look odd. I ended up trimming so that the wood part was the same thickness as the marquee retainer, for even lighting.  

[BobA]

Just make sure your marquee is centered and has little or no graphics on the area where you fasten to the mdf.   Most marquees have a retainer covering much of this area.