The pushpins are a integral part of creating a route. If you don't have them, TransDEM can't create a DEM of the route because it doesn't know where the route is. They are located in the Southwest corner of the image because that is where TD looks for them.
For a Northwest to Southeast route, position GE at the upper-left. Depending on how many baseboards away from the track you plan to have images, move approximately that distance away from the track North. Put a pushpin in the lower-left corner of GE (the southwest corner). Use the down-arrow key and move the display down until the pushpin is at the upper-left corner. Put another pushpin in the lower-left. In a similar manner move south until you have reached your baseboard-away-from-tracks limit.
Go back to the topmost pushpin using the up-arrow key. Now, with the pushpin sitting in the lower-left, click and HOLD the mouse when it is hovering in the lower-RIGHT of the image. Drag the mouse to the left until the mouse pointer is approximately where the pushpin used to be (in the lower-left). Release the mouse and be sure to hit the "N" and the "U" keys before placing a pushpin where you left the mouse.
Using the "click-and-hold" procedure, you can move the GE image east, west, north, and south easily, always making sure you release the mouse in the lower-left corner and put down a pushpin.
To see how you are doing, use the mousewheel to zoom out until you can see all (or some) of your pushpins. Gauge where you need to go next and double-click the closest pushpin. GE will zoom back down and end up with the pushpin in the lower-left. Now you can click-and-drag the image in the direction you need to go.
It all sounds complicated, but give it a try in a dry run until you are able to figure out which way you need to drag GE in order to capture the next tile in line. Always remember that you need a pushpin in the southwest corner for the tile to be generated.
Bill