You could make a two copies of your family tree. On one copy delete one side of the family and on the other copy delete the other. I would definitely keep the original family free with everyone on it.
You might also consider exporting your GEDCOM file (family tree), importing it into a program that will let you export a portion of your family tree, then importing those portions back into FamilyEcho. Here is a page that talks about how to split your GEDCOM file (family tree) in a number of different family tree programs.