Hi Samuel
I just went through this exercise with a client, and I argued strongly not to merge the datasets. I won. You REALLY don't want to manage multiple companies using Ledger departments if at all possible - the chances of miscoding are enormous.
The key is to find out why they want to merge the datasets. In my case the companies were in the same business with the same customers, but in different areas of the country. They transfer inventory back and forth between companies, and they want to see a consolidated customer lookup.
Since you didn't mention inventory, I won't go into how I worked around that one. As for consolidated customer lookup, I created a GridView to do it. They purposely use unique customer codes for each company (so they know by looking at the code which company it is), so the GridView prompts for the phone number.
On the plus side (for the client), merging uses up fewer Lanpaks, but on the negative side, there are going to be more conflicts when posting. Security becomes problematic. And in my client's situation, the clincher against merging was that Invoices/OrderEntry can have only one series of invoice numbers, which was unacceptable.
In any case, a customer can only be linked to one Control Account Set, so the same customer must be entered once per company in order to track Receivables at the department level.
Steve