I think the current version of Brother's Keeper is 7.5 so you would probably want to download the update before you start importing gedcoms.
It is a good while since I did anything like that, but on my BK if you go to Gedcom > Import that has a big warning about how all the newly imported individuals will just be added and not be checked for duplications, or how to keep them as a separate set. (you need to make a new folder first, before putting the new data in it.) Then whenever you want to change from one line of descent to another you go to 'open database' and pick the other one.
Afterthought - there is a disadvantage to having different families in different databases. Using Edit, Find, Select person will only list the people in the currently open database. It cannot produce a combined list of people.