Designing in Adobe InDesign CS5 for the upcoming Adobe Digital Publishing Suite entails creating a document that's 1024 x 768 pixels or 768 x 1024 pixels. But the Adobe Viewer obscures a 6 pixel vertical region on the right side of the screen with a vertical scroll indicator, and the Viewer "chrome" that appears when the user taps occupies 44 pixels at the top and bottom of the screen.
I've created a couple of simple CS5 template files, one for each orientation, that mark these regions with guides, have the measurement system set to pixels, and the transparency blend space sent to RGB. For more information, read the explanatory notes on the pasteboard of page one in the templates.
You may download the free templates here. I hope you find these useful!