There’s something important that is getting overlooked in all the coverage of the stunning news that Bank of America has had to line up $20 billion in assistance from the federal government to handle problems at Merrill Lynch, just days after closing the Merrill purchase.

That something is this: The problems are just beginning.

The losses on mortgage-backed securities, which BofA now realizes could top $100 billion, are just one of the reasons that we wrote in September that we didn’t like the Merrill deal. The losses may actually be relatively easy to take care of, because the federal government is desperate enough to shore up the U.S. financial system that it will help BofA with the mortgage-related losses. But the government won’t help when BofA has to sort out the clashes between the white-shoe Merrill brokers and BofA’s more middle-class culture–and various newspaper reports say those clashes are already well under way. The government also can’t be expected to help BofA when it turns out that becoming a financial supermarket–with retail brokerage, investment banking and trading operations, on top of BofA’s retail banking–isn’t a viable strategy. Citigroup just spent a decade trying that strategy and is now reversing it, causing great pain all around. Why should BofA’s supermarket work any better?

Stay tuned. More bad news is coming.