You may find it easier to “merge” same-sex married couples during the data extract creation process. See this answer for more information on utilizing the Attach Characteristics option to create spouse variables.
If you prefer to merge same-sex married couples in STATA, you could create a dataset of married same-sex householders (SSMC>0 and RELATE=1) and a separate dataset of same-sex spouses (SSMC>0 and RELATE=2). You could then merge these two datasets together using SERIAL to uniquely identify same-sex couples that belong to the same household. Keep in mind that same-sex married couples can be identified using SSMC and RELATE in the 2013 ACS sample only.
Hope this helps.