Wow. So many questions, that I'm not going to quote them as it will take too long! I do sympathize. Since I downloaded and reviewed the 'advanced' manual that you found here:
http://www.archicadwiki.com/EcoDesigner ... User_Guide
I actually have more questions rather than fewer, myself!
Do NOT click the button to analyze your model after you have made any changes in Model Review (which is almost always necessary)... it takes you back to the beginning, as you saw. Only do that if you have made substantial model changes and it would be faster to reanalyze and change rather than use Model Review to add in or change the modified elements.
The Advanced Guide describes the issue with basement floor vs slab on grade and how to deal with each. However, I was a bit confused in the way that the guide mentioned that the ground level entered in the first screen is used in this calculation... since the ground may well be sloped or stepped. (Early in the guide, it says to use the average grade ... but that's not very accurate for a two-stepped structure on a sloping site where you would want the average for each part. Perhaps in a case like that one needs to analyze each part of the building separately.)
Trees and real shading effects (roof overhangs/etc) are discussed as well ... and that they do not intend for ED to have that level of detail. It does not calculate solarization according to the manual. Thus, the shading values for each facade ... described in more detail in the Advanced Guide (although the numeric value for shading is not quantified in a way to help us know what a sensible number would be were we to want to change things... ditto other numeric values that are basically presented as "here they are" without any units or means to tie them to reality or design intent. I have to assume that the Advanced Guide is a first draft rushed out after I posted the customization article on the Wiki and that it will get edited and fleshed out in time.)
The Advanced Guide also suggests ways of treating unconditioned spaces.
No, you never have to delete anything from ArchiCAD to delete it from the ED building volume. Again, Model Review is your friend ... and essential to understand well. If auto analysis included some structures that should not delineate the building volume, then just select them and clear the highlight. They will then be ignored. Yes, if a wall serves multiple functions, you need to split it in ArchiCAD so that in Model Review you can assign different attributes to it. But, that's how your model should be built anyway.
Unconditioned attic space is described in the Advanced Guide.
Do not know what you mean by 'exterior walls protected by roof'? If you mean that they are shaded, then no. If you mean connected to form a volume, then yes - see Model Review and modify as required with the palette.
I believe that there is a problem with vaulted (cathedral, non-cubic) spaces still and that ED does not compute the volume for them properly.
Back on Model Review... your customization is saved with your file, so it does not need to be repeated. Be sure to say 'yes' to save things.
Telling ED what layers things are on would not really help ... in that ED attempts to intelligently locate enclosed spaces. Some external walls might not enclose a space. No reason to make modeling and layer assignment more persnickety IMHO. If auto-assignment and model review do not quickly describe your exact building volume, then you should post an image so that the ED team can see where there is a problem. Do note! If you have made your model with multiple walls to represent skins (sheathing, finish) etc rather than use a composite, then getting them all assigned as external with proper insulating values becomes a mess... as ED combines the thickness of the wall with the insulative properties to obtain the insulative characteristics of the wall. Also note that it says that ED does not handle complex profiles walls well, which is a shame since I use them for almost all exterior walls and many interior ones.
I do think that Graphisoft would do well to create a tutorial file with a building more complex than the slab-on-grade box in the User Guide and walk us through every step of model review, assignment and analysis, discussing the options and trade-offs along the way. It needs this to be a complete 'product', ready for customer use I think as I think every one of your questions is reasonable and should be answered as part of a methodical case study.