Will I mess with Authorship if I setup multiple client websites under my Webmaster tools login?
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I currently have a dozen client websites or so that I have setup under my Webmaster tools login. Should I put them each separately under their own webmaster tools, then just add me as a user? Is the way I'm doing it now messing with Authorship?
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You should be just fine with G+ authorship as long as in the clients' pages you have the rel=author links in there.
Yes, there are alternate ways of establishing G+ authorship, but it's my understanding that the explicit 2-way links are the core means of identifying the author-document relationship, and that the alternate methods are just that.
I think it's pretty safe to verify these using Google's own structured data test tool. Yes, it has a few bugs, and fails to read some websites, but it's overall pretty reliable, and I would expect that it's using a very similar bit of logic to determine authorship that the SERPs-producing code is using.