If your tools lack that feature, I'd suggest to find something that will work.
If you're looking for suggestions, Google is your friend - I see Kinemac & Cheeta3D, but I know nothing about them, sorry. Try the Mac App Store. Keynote from Apple has certain 3d capabilities, but what you use may depend on budget, skills and specific modeling involved...molecular, mesh needs, etc. using Maya, Cinema4D, and (the free and open source) Blender.
I'm aware of that, that is why I wrote "Can I open the dae file in another program and set the start position there?".
I have googled and came across this page http://en.wikipedia.org/wiki/COLLADA, it list the tools you sugest and I have tried both Blender, Carrara, Chnema4D, Maya. However I couldn't figure how to open/imort the .dae file.
I seek much more specific help than you seams capable of providing in this specific case.
1) How do I in iBooks Author set the camera position manually.
The documentation says: "be sure to add a camera to your object. This will be used for the default view in your iBooks Author book."
default indicate that there are other options in the iBooks Author program.
If this is not the case:
2) What is the prefered program for createing 3d model with a start camera position.
2a) More specific how do I do that in the program.
Note that is is unlikely that any other forum can answer question 2, since this is compatibility specific issue between a 3d program and iBooks Author.
Obviously I'm late to this thread, but I ran into the same problem this morning and created this work-around since I don't have the time to explore much outside of SketchUp8. Hope this helps: http://sketchup.google.com/3dwarehouse/details?mid=de262856580e80834b892bc5603ca b56