Dave, here's a good FAQ for scanning your cover in at 300dpi:
Scanning instructions, etc.
But the key bit of info not included in that is that after you've scanned the cover, and you've got both the blank template and the scanned picture both open in photoshop:
Select the scanned image. Go to Photoshop's Layer menu (do you see the Layer menu? If not, go to WINDOW > SHOW LAYERS. There it is!) Now just grab the layer (put your mouse on it and click down and stay down) and drag it over, quickly, to the mostly blank .psd template. If you do it quick enough it will magically appear there on the template. Don't worry if it is off-center (or wildly off center) - we'll handle that later.
Sometimes you need to practice a bit but the concept is you just drag it over from one image to another, no different than dragging & dropping paragraphs in a Word document really.
You can ignore the scanned image now, from this point on I am just referring to the .psd (the template which now has the scan, waiting to be tweaked into shape to fit a ThinPak).
EDIT > FREE TRANSFORM. You can now move the image around within the template, so please do so. Move the image patiently and carefully so that the _front_ cover is exactly where it should be. Don't worry about the spine being too wide or the back cover going off the back edge, just concentrate on the front cover being where the front should be. Good. Press enter to let it know you're done with moving it around.
Now let's do the back cover. Go to LAYER > DUPLICATE LAYER in the top menu that runs across the top of the screen. You've just made a copy of that whole layer, front and back, though you wouldn't really notice if you didn't have the layer menu open, which now shows a new layer exists. All we really need is the back but we'll delete the extra front later. Gently slide this layer so that the BACK cover is perfectly where it should be.
"But...but...this covers up the front cover! Now the front cover is going off the edge!" you protest. Well indeed, so get rid of that right-half of the image (I mean, the redundant front cover which is now wildly off) by using the rectangular marquee tool (the same tool you use to crop photos, but in this case you're NOT cropping the whole image, you're just going to select the right half of the image and simply press the delete key, so you can see what's underneath. And what is underneath is of course the properly aligned front cover which you did earlier.
So now you've got the back cover where the back cover should be, and the front cover where the front cover should be! All you need now is the spine.
I think you can figure out where to get the spine from on your own. They key is that the spine should be a layer of its own, just the vertical strip of spine above the other layers. You can then either squish the spine layer (using EDIT > FREE TRANSFORM and grabbing the edges with your mouse) so it fits the ThinPak spine, or painstakingly rework it, your choice.
Save this under a different name (like "Porkys2.psd"). Print it.
This may sound complex but it really only takes a few minutes once you know the drill.