It's automatic. If you install UT 2.1 on the same PC where 1.x was already running, it'll reuse the data files. I would make a backup of them first just in case things don't work out.
C:\Users\<USERNAME>\AppData\Roaming\Unitrunker\
Also keep in mind that 2.1 only works with certain dongles. There is no support for scanner control or discriminator taps.
Read here if you haven't already before proceeding:
http://www.unitrunker.com/v2/