Two diffrent databases can not be combined together.So one has to sacrifice.
Lets say Site A has 100 client and site B has 50 clients.
all are installed and working properly...now you decide to combine both these SEPMs.
So what you can do is.Export the list of IP address for the clients in site B ( only because they are less--so I wont consider this site as main site )
Then either Run Management server configuration wizard and select Add replication parter and connect to SEPM on Site A for replication.
Or Un-install SEPM on Site B ..install fresh and select Add a replication parter.
Once SEPM is installed and both Sites are replicating Use SylinkReplacer Tool ( for this tool you will have to contact support --This tool remotely replaces sylink.xml files on client machines either by selecting list of IP address or by selecting a range of IP address ).
Use Sylinkreplacer to connect those 50 clients in SIte B to the SEPM.
Once this is done it will become centrally managed.then you can apply Management Server list on the clients groups ( Clients in which group will report to which SEPM ).
Note :As mentioned above even if you choose management server configuration wizard it will wipe out the current database.