Yes you can use multiple domain with EEM for authentication or sync with SDM.
Here is a quick doc about how you can setup EEM to use like "Proxy" ldap server with multiple domain.
First you have to configure a proxy server for EEM. (Normally on the same server as your EEM installation) (file EXEMPLE.DXC from my zip file)
Second
Secondly, you must add the number of AD instances you want to process with your proxy server. (file EXEMPLE.DXG from my zip file)
Subsequently, you add the number of domain ldap that you wish to be able to process by your proxy server. (file EXEMPLEAD1.DXC, EXEMPLEAD2.DXC etc.)
Once the proxy server is available and online (just to follow the document as an attachment) you must configure directly in EEM the use of the new proxy server (it in the file EXAMPLE.DXC)
Afterwards, in SDM you have to change the configuration of SDM to use the new proxy server that you just created with EEM. EEM will do some kind of cascade query through the various ldap directory you have added (EXEMPLEAD1.DXC, EXEMPLEAD2.DXC etc.)
I used this configuration for several years with 2 different domains during an acquisition. I even kept this configuration of the proxy server even though today the two domains are merged. We never knows when the next acquisition;)
I hope I have answered your question. Do not hesitate if you need more information.
Thanks
Rémy