Administering the first SEPM domain that I have imported our AD domain into, Im able to click on Servers (under Domains), right click the primary AV server and shoose properties then click the directory servers tab and see domain controllers from both Ad domains.
Administering the second SEPM domain that the second AD domain was imported into and following those same clicks as above, im able to see an identical Directory Servers window.
When you say login, do you truly mean log in or jsut change the administration form the single console? We only have one instance of SEPM running with 2 SEPM domains that has 2 AD domains imported into them.