First you need to create your route. You can do that from the Find User Routes Near your Trip page by clicking the "Create New Route" tab, entering a route name, and then putting in your start and end points.
Once you have a route created, you'll need to run a pocket query on that route. From the same Find User Routes Near your Trip page, click the "Your Created Routes" tab to view your routes. Then click the "Create Pocket Query" link next to the route you want to use. Next, you'll see a form with all the search options for cache options and distance from your route to search.
Submitting the form will generate a .gpx (by default) or .loc file that you can use on your GPSr. To see the list of caches your query generated, click the "preview the search" link on the confirmation page--it will be in light green text below the map. On the list of caches page, you can also click the "Map this Location" link to view the caches in a map a long your route.