The problem with using MapRun under bush canopy is that control sites cannot be seen on Google Earth. They have to be precisely GPS way-pointed on the ground in order to be reliably used in MapRun. In addition MapRun is better suited to score or scatter events than to line events.
Here is my document describing my approach after running a number of events like this. (The software is not yet available for download but I’m happy to do the conversion for you.)
Here is my post about super accurate GPS waypointing.