The only thing I do is to highlight the freighter and right click the destination planet. I don't think there's a screen to automatically program trade routes.
Once you do that initial trip from the planet that built the freighter (the source) to an alien system (the destination), the trade route is set and will be handled automatically by the computer. All you have to do is sit back and watch the money roll in. The route will remain up even if the destination system changes hands to another alien civilization, but if you take over the target (through any means) the route is cancelled. I got a nice kick in the economy my last game when the Altarians surrendered to me after taking a horrible beating from the Vox and thus took down seven routes, but it was endgame so I just rode it out to tech victory.