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Amazon's Kindle still isn't ready for comics and I'm not sure how they're apps handle graphic content. Might want to download their free reader software and demo some comics to see how they look, might help you figure out how you want to format your book for their system.
Comixology is all but impossible for an indy to get into right now, but they are releasing their formatting process to make them more accessible. It's only to select publishers right now, but I understand they will be opening it up to everyone soon.