If you want to incorporate the entire Template brain to your new brain I would actually:
You can easily manually select thoughts and copy them, or export them to TheBrain XML format, but selecting tags and thought types requires manual selection and can take a while. If you don't use types or tags you can just: Create a Brainzip of your template brain (File > Create Brainzip). Extract your Brainzip to a different folder then your template brain. Choose File > Rename Brain and name it. Choose File > Utilities > Assign Brain New Guid (this insures it doesn't conflict with synchronizing to WebBrain with your Template brain). Choose File and towards the bottom (where it lists your recent databases) choose your template brain to open it again. Move the .brain file and _brain folder of your new database to where you want it to reside. Choose File and in the list at the bottom, choose the brain you just created. It will say it didn't find it, and do you want to remove from the list. Say yes (this keeps your list clean). Choose File > Open Brain and browse to the location you just moved your new brain to. Dun!
From the Report tab, make sure it is set to all and hit the refresh button Choose Edit > Add Report Results to Selection On the selection window, right click and choose Copy Selected Thoughts In your new brain, right click the plex and Paste Thoughts.