Well I like to start with the campaign map, I dunno if this is the best way, but you can make the campaign map with a minimum of factions/units. Once this is done, you can then modify the factions and place them on the map, then finish off with the units.

But you can start from the other end with no difficulty. You just decide when you start which factions will become which modded factions, then start adding units to them. Then you can edit the factions, and then make the map.

Really it doesn't make much difference. Do what takes your fancy.