If I understand you correctly, what you are trying to do is have ONE family tree file with multiple separate branches that aren't linked within the tree. I use FTM2012 and am doing the genealogy of a town, so have one tree with several hundred separate families lines in it.
To add an individual person who is not connected to anyone in the tree - Go to Person > Add Person > Add unrelated person.
If you want to merge trees, just do a standard merge process, it doesn't matter that merged tree has no linked individuals.
I originally created my tree on Ancestry.com, and created a ficticious person "Town of Washta" with gender unknown and no birth/death dates. Then I added the top of each family tree as a child of this ficticious person. Once I had all the tops of the individual trees added, I just deleted the ficticious "Town of Washta" person and then had all the different families in one tree. As I discovered marriages and relationships between the families, I just created the relationship link between two people in the tree.