I'm with you - I am going to start taking some pictures today on my 75% done build and need to figure this out for my own A495's. So I'm going to put my thoughts down here and hopefully it will help you as much as it will help coalesce my own thoughts.
Here is a thread where some people are discussing pictures straight from the camera and tweaking camera settings for a better picture. http://diybookscanner.org/forum/viewtopic.php?f=1&t=917
In general my understanding of initial settings are:
Try and get the camera into manual mode so you can set the right properties. If you leave it in auto it may be out of focus on mostly blank pages, and it would take longer to actually take the picture while it does it's auto functions. Also leaving it in auto while you are taking pictures of a 500 page book can really stress the mechanics of the camera and cause it to break down sooner than you would like.
Focus - manually focus on the page if possible. You MAY have to re-focus as you get to different parts of the book because the page thickness will cause the book position to shift relative to the camera - unless you have the camera mounted in a fixed position relative to the platen then you wont have to re-focus.
Aperture - as small as you can get it (the smallest hole possible). That will give you the largest depth of field - which hopefully means that the entire page will be in focus at the same time. An aperture of f/8 is a smaller hole than f/4.
Shutter speed - As fast as possible to preclude blurring from camera shake or vibrations. I think people are using around 1/60 of a second or less.
ISO - as "fast" a film as possible. There's a lot that goes into the theory of ISO numbers - mostly having to do with actual physical film cameras. Since we use digital cameras, the ISO number is mostly a way to simulate the effects of real film - but the faster the ISO, generally the fewer artifacts on the image. Try using ISO 100 or 200 to begin with - or whatever the lowest value your camera uses.
All these settings require A LOT of light. If you take a picture and it is too dark you can try slowing the shutter speed, but if it gets out of focus from vibrations then you might need to slow down the ISO or open the aperture a little bit. Adjusting your EV to slightly over-expose might help, but I'm not sure if that is possible when you are in manual mode??
Using full resolution is OK to start with. I have heard people say that anything over 300dpi isn't really that helpful as it takes the software longer to process it and you aren't getting that much more bang for the buck. If you are taking a picture of an 8"x10" book that would be 2400x3000 pixels or 7,200,000 pixels (7.2MP) Your camera should tell you what "quality" (normal, fine, super fine) gives which pixel count. Select the one that give you at least 300dpi for the size book you are using. Daniel Reetz made a comment on one of these threads that if you set up your camera to take a picture of the entire usable platten area at 300 dpi, then whatever book you put in there will be 300 dpi. Then you just have to crop the unused parts of the picture when processing.
Macro use would depend on how far your camera is positioned from the platten. I'm not sure about this one, but I would think that you wouldn't need macro mode with a 14.2MP camera.
I don't think you would need the DIS. Your camera's are not being held by hand, so they should be fairly stable to begin with. If you are consistently getting shaky pictures that can't be corrected by speeding up your shutter speed, then try it and see.
I plan on using a white card (or grey card if that's what your camera needs) to get a custom white balance for the actual lighting conditions. You should only need to do this once at the beginning of each scanning session. If your build includes some kind of shroud to keep out external light and use ONLY the light you provide, then you should only need to do this once. Just remember that ALL lights will change over time. How often you would need to re-check the light levels depends on the quality and type of light you are using and how long the lights are actually on.
Now that I wrote all of that, here is a little thing I just thought of. You could try setting your camera to full auto and let it take a picture. Auto cameras use all kinds of math formulas to determine "A" correct setting to get proper exposure. There are many combinations that will give proper exposure, but the camera will give one. If the picture is generally acceptable, you can check out the EXIF data and use those settings as a baseline to adjust as desired.
I hope that helps - and remember - this advice comes from a totally anonymous stranger on an internet site and you really have no idea if I know what I'm talking about!!
Really though, this is my understanding of how things work - but if anyone can correct any errors, I'd really appreciate learning more!