Craig,
Nice layout! While I'm no expert on digital photographer, I have learned a lot about taking shots of my own stuff by the examples right here on the MLS. One thing I noticed in the really good shots are that the ground cover around the track is always cleaned of any large leafs.
A large familiar object in close proximity to the train tends to spoil the effect. I have this crazy willow tree outside where I take my best shots, and when the wind blows, no matter what season, those leafs fall in the hundreds on the track and models. I don't take shots on windy days because I'd spend most of my time picking leafs off everything.
I also noticed something about focus; I have 3 digital cameras, a 5 mp pentax and vivatar and a 6 mp Cannon rebel. As Jason pointed out, most digital cameras have a setting for auto focus that can be disabled. I noticed on all 3 of mine that I can focus automatically on specific areas I'm interested in by pointing cross hairs in the viewer on that place and holding the shutter button down half way. That works on all 3 different products.
In addition there is a button that has lens type settings for distances; each camera has a portrait setting, a closeup setting, a wide view setting and an action setting. Each camera also has a setting for light and speed,,, although they aren't the traditional f stop and shutter speed on the vivatar or the pentax, they give you a flash option on or off and a backlighting and front lighting setting.
You may want to check the manual on your camera for those buttons and options.
I find that in low light days, it is best to use a tripod. You can buy a good enough tripod for about 39 dollars and it is well worth the investment if you are going to take pictures. Even though an object may look focused through the lens, you will find it out of focus if you are taking shots in low light because the digital camera adjusts the shutter speed and the aperature to allow more light to come in. Since the speed is slower in low light, even your pulse will cause a small enough vibration to cause the image to appear a tiny bit out of focus. It looks like you have a lot of shade on your layout, so you may want to invest in a tripod or two. One for higher views and a smaller 6 inch tripod for your ant views.
Finally, the larger the amount of mega pixels you can take the better your shot will be for two reasons. I noticed that the lens on each of my cameras varies slightly in that my pentax is really good on well lighted close ups of objects, my vivatar is passable on all settings and my Cannon excells in all but is best on distance shots.
Since the Cannon has 1 mega pixel more than the other 2 I can get most of a shot in pretty good focus by standing further away from the train and including more of the foreground. I then take the image into photoshop and crop out the foreground and background and get a fairly well focused shot of just the train and its immediate foreground. Not sure if that makes sense or not, but basically what I'm saying is, if you have a camera with at least 6 mp of resolution, you can set the camera at its highest resolution and stet the camera 6 feet from the object and get a better focused image of the front, and back of the train than you could if you set the camera 4 inches from the train. So some of my best closeup shots are actually taken from 6 feet away.
I know there's probably some explanation for this, all I know is it works for me.