The way Google says to handle it makes me think they don't appreciate iframes that much.
Google supports frames and iframes to the extent that it can. Frames
can cause problems for search engines because they don't correspond to
the conceptual model of the web. In this model, one page displays only
one URL. Pages that use frames or iframes display several URLs (one
for each frame) within a single page. Google tries to associate framed
content with the page containing the frames, but we don't guarantee
that we will.
From my experience, if you are showing inside an iframe, information that is indeed important and related to your original website, you'll be basically spreading the strength of your content.
There's some discussion about it here: https://productforums.google.com/forum/#!topic/webmasters/uQ8m1RPqgxw
Other article I found, says this:
However, pages that utilize iFrames display multiple URLs for one lone
page, as every single iFrame has its own different URL. This is where
the problems begin. When Google crawls webpages with iFrames, the
search engine attempts to associate all the framed content with the
parent HTML document, or the page that contains all the iFrames. As
great as Google is, it isn’t perfect and it doesn’t always succeed.
In MOZ there's a discussion about the subject that might be interesting: http://moz.com/community/q/iframes-seo
The best way to optimize the iframe is actually have the least content possible there. What I mean is that if you have a big page with text and a Form, try to remove the text and leave only the form while inserting the content on the original page.
There's no way to tell Webmaster Tools you have an iframe, however there's nothing forbidding you to add it as a new property.
My advice: don't use it unless you're really forced to.