I'm not sure exactly what you're asking, but I think I get the majority of it.
I have found that yes, it is best to have one tree with all of your information in it. I used to have two trees, one for my mother and one for my father. I joined them together and have been happy that I did.
It is very easy to import GEDCOMs into a file. I would start with a new file and ask Roots Magic to find one of the GEDCOMs, then import the second one. Doing this will not delete or destroy your original files.
Then you can find the duplicate people and merge them. I would make a backup of your new file before merging any people.
It is also easy to split off branches to give to other people or print reports. Splitting off a branch is under the export file option.