Okay, so for Warhammer Total War I had, say, two sorts of chaos warrior. Same model, but one has red armour and berserks, one has blue armour and gets druid chant.
So what I do is make the DMB entry as I usually would for blue-guy. Then I add a merc line to the skin, as if I was going to make a mercenary unit with that model as well. But the merc skin I put in is red-guy.
I then make both their entries as normal in DMB with their costs, statlines, etc. And I give them the same battle model, but red-guy has the mercenary_unit flag. The key thing here is basically just that so far as I can tell the mercenary_unit flag in DMB only does three things:
1. Makes them use the merc skin for the unit model rather than the skin assigned to whichever faction owns them.
2. When you select units in custom battle, mercs will be at the end of the roster rather than with units of a similar type.
3. You can
if you so wish then add the unit to a mercenary pool on the campaign map, but you don't have to.
You can train units with the mercenary_unit flag from buildings like any other and give them to factions in custom battle like any other.
Does that make sense? I can post code examples if you want.