Fresh install under WP2.8beta-1: View looks right but tried to set options for initial setup and got
http: // domain/wp-admin/themes.php?page=functions.php cannot load

Is this happening when you try to set Atahualpa as the theme?
Have you installed any other theme and gotten it to activate?

Re-upload fixed activation.
I see mid-col and choices of left/right/both sidebars.
Can config make 2 right sidebars? If so, covers most aps I can think of. If not, I'll have to keep more than one theme around.

I beleive if you search the forums, there is an explaination how to modify the code to accomplish that (2 col on right). Having this as a theme option (vrs editing the code) is on Flynn's to-do list for 3.3.4
You might want to make him a donation to 'urge' that option.

I'll look for that.
One bit more, re Blog Title and Blog Tagline, in HEADER options:
trying to put space in front, to get text off border -- none of these work, margin, padding, '& nbsp ;' or space character.

Are you talking about Overlayed Blog Title on the header image, if so see the settings in ATO-> Header image->Overlayed Blog Title/Tagline Style