The little blue and yellow dots on the vessel are where the nodes are. As you select one, either from the menu, or from clicking on the dot on the 3D image, you'll "highlight" it's respective part in the other portion of the window. In other words, you click on "Node: 11", and you'll see where "Node: 11" is on the ships, by looking at where the little red, yellow and green orientation marker lines are situated on the ship. If you then click on a different dot on the ship and get the marker lines to move, you see that the left-hand menu has now highlighted your choice... I had a picture of that on here somewhere not too long ago, but alas, I think it's on Photobucket, and we don't stand a chance of retrieving it there...
Nothing but the "main" node selected and the "Model preview" selected:
One of the engine exhaust nodes selected by clicking on it's node listing on the left-hand menu:
The Conning Tower's "mount" node selected by clicking on the yellow dot on the 3D model:
Easy peasy. Now, as for editing... I know how to delete stuff... If you need help with that, just call me. Only other things I know how to use on the model preview is the keyboard arrow keys, and the mouse wheel to zoom in and out, and the right-click and drag to move (in conjunction with the arrow keys). It takes a bit getting used to the "backwardness" of the controls, maybe... - Oh! and those little lightbulb pushbutton menu thingies (Windows calls 'em "tiles"), they can do your texture (sometimes) and shading...