In Google Webmaster Help there is a straight forward question and answer about how to handle M-dot (i.e. m.domain.com sites in Google Webmaster Tools.

In short, an M-dot is a separate site and should be verified separately in Google Webmaster Tools.

Zineb, a Google Webmaster support representative answered each question:

Furthermore, she answered the question on a separate mobile domain.

Forum discussion at Google Webmaster Help.