Difficult to show from photos Nate as the two pipes that go upwards run in behind the shock but I will try.
This photo shows where they come out and the gold connector that fastens underneath the airbox bolt.
This photo shows where they run upwards from the carb.
The pipe on the right of the photo runs down between the engine casing and frame if I recall correctly. The left-hand one runs forward and into the clip on the emulsifier - see photo below.
Make sure that your one-way valves are clear of debris and working properly before you re-install the pipes. There should be one at the end of both breather pipes. The pipes are open at the top - something to be aware of if going through deep water!
Does that help? If not maybe put up a photo or two to show where you are running yours for us to check