Import each of the Guitar Pro tracks into different tracks in EOF. Then you can copy and paste notes from one track to the other, just make sure to use appropriate seek controls (ie. the Pg Up/Dn related ones, all of which are listed in Song>Seek) so that the seek position is where you want the pasted notes to go before you paste them. You can copy and paste between different instances of EOF, but copy/pasting within the same instance of EOF is better because it will also copy certain types of techniques that may have imported from the Guitar Pro file. Tech notes that were imported would have to be copy/pasted separately from the regular notes. You can check to see if there are any by pressing F4 to toggle "tech view" on or off. Pasting tech notes is a little more complicated in that you would need to move the seek position to the correct note where you want the paste to begin. Depending on the notes being copied, the first normal note wasn't necessarily the first of them that had tech notes, so you may paste the normal notes at one beat, and then paste the normal notes farther ahead in the chart.