What Family Tree Maker does, is to Create Files. You enter individuals into that file or files.
Its the Relationships between the individuals that create TREES. Depending on where you are or who you have selected, there will be a Tree. Move to another individual, you would have a Different Tree.
When you select an individual, you will actually have Two (2) Trees. A Descendant Tree and an Ancestral Tree.
That is why I am asking you what is a tree. Just trying to understand the problem.
So, you created a "dedicated tree for the Scotts". I think that what you created was a Family Tree Maker FILE that included Scotts. Again, moving around that file, you will probably have multiple Trees, depending on where you are in that tree and whether you are looking do Ancestors or looking at descendants for that individual.
If there is a Relationship between a Scott and a Macdonald AND you have Two Files, you wouldn't see that Relationship. OR you would have to manually add the ancestors of or the descendants of the person who had the relationship with the other file.
The TREES come into play, more clearly, when you work with the various options in the Publish Workspace. That is, creating Charts and Genealogy Reports.
Keeping the information in Two Family File, if you were to look at the Kinship Report, you wouldn't see the relationship between the Scotts and MacDonalds.