FTM allows you do create multiple trees. Just go to the Plain workspace and create a new tree.
You said you wanted to keep the trees separate until you find the connection. If everyone is in one file it is easy to make the connection using Attach. If the lines are in two separate files you would have to use file merge. This can be tricky and create a lot of problems and a big cleanup job. At least that is my experience the one time I tried to merge files.