When a User is logged in to Match My Email and viewing the Email Cloud, they can manually match multiple selected messages to Salesforce records of their choosing. To do so, when in Email Cloud, check the box to left of messages to select them. Click the Match command button.
In the Match pop-up window, type into Records field begin to type in a name associated with the record.
In the screenshot below, Superstorm is typed in and the Opportunity record with that name is found. Click on the option to select the record you want. If these emails should be manually matched to another record, another Record field will show in which one can type again. Otherwise, click OK.
All of the emails selected will then be matched to the desired record(s).