Before you create the junction in the old location, you move the folder to the new location.
For example, if you are wanting to move
C:\Cakewalk Content
C:\Program Files (x86)\Cakewalk
C:\Program Files\Cakewalk
to
E:\Cakewalk Content
E:\Program Files (x86)\Cakewalk
E:\Program Files\Cakewalk
First you copy the data to the E drive, and then you create the junction by opening the command window and running...
mklink /J "C:\Cakewalk Content" "E:\Cakewalk Content"
mklink /J "C:\Program Files (x86)\Cakewalk" "E:\Program Files (x86)\Cakewalk"
mklink /J "C:\Program Files\Cakewalk" "E:\Program Files\Cakewalk"
At this point, everything works exactly like it did before. Cakewalk doesn't know you've moved the stuff.