How many people are there in total in the 20 trees? FTM can be used without a loss of efficiency up to about 20,000 people. FTM can be used beyond that, but speed will start to slow down.
I take it that when you say "overlap", you mean inter-marrying of people between the 20 trees.
I suggest you combine these 20 trees into one tree and leave them that way and record the intermarriages between the trees. This way will show full ahnentafels and full descending charts and reports.
I have worked on a area genealogy that is up to about 15,000 persons and find that 75% of them are all cousins to me as we share ancestors from the 1600s; some in multiple ways. I could not visualize splitting these people into separate files for purposes of the area genealogy. I have occasionally split the file for reporting or exporting purposes when a view of one slice of the area genealogy is wanted.