>How do we handle these?

**TL;DR**: We do not. 

Only SE Employees can handle this now.  
They only handle requests from the user who created the two accounts.

You can leave a comment for the user, but if they're careless enough to create multiple accounts it's highly unlikely they'll go to all the effort required to merge account.

**UPDATE**:  
Let the backpedaling being... Now Moderators can fill out the same form on behalf of users when the users, who weren't likely to come back in the first place, never request it themselves. So Moderators can jump through more hoops tha before, request an *Official SE Employee Stamp of Approval™*, and get'r done... again