What type of track file does the GP-E2 create. You can import track files into Aperture and then set the images to the track.
See Importing and Working with GPS Track File Data and Aperture 3.x: Importing and Working with GPS Track File Data to see if doing it this way meets your needs.
If you set your GP-E2 to the mode where it also records GPS tracks by turning the three-position-switch on the top of the unit to the "LOG" position, the GP-E2 will then also record GPS track logs. Use them like this:
After you come home when you're done shooting, use Canon's MapUtility software that came bundled with the GP-E2. With MapUtility running and the GP-E2 connected to it you can import the track logs by clicking the "GPS logs" tab on the top left corner and then clicking "import from GPS device" on the bottom left. When you have imported all tracks you need, close MapUtility! Then, in the Finder, navigate to /Macintosh HD/users/yourname/documents/Canon Utilities/GPS Log Files/ where all the log files are stored in a very common NMEA-0183 format that are readable by lots of GPS capable programs including Aperture.
In Aperture click on the map view button or press shift-P. Below the map click on "GPS" -> "import GPS log" and point to the location of your track(s) as found above in the finder. When the track shows up in Aperture, drag one picture on the correct location of the track. When you let go of the mouse, Aperture shows a message in the bottom of the map asking if it should line up the other pics on that same track according to their date/time references. Click OK and you're done.
Hope that helps!