SEO Implications and indexing with A/B Testing Plugin

I'm curious as to how the themes should be coded, not to be penalized by the search engines. We are testing a 1 page theme ( vs. a traditional paged theme ( **note dev. has not been deployed or configured in the production environment. Both themes will run from Is is safe to place a noindex in the head of the the paged theme and use canonical to indicate all urls of the paged theme point to the 1 page theme.

Does this plugin instruct GoogleBot to look at a particular theme? If so, are there cloaking precautions?

We want to ensure our primary theme is not penalized by the search engines by potentially serving different markup.

Any information would be appreciated.