Modules
Ok, Modules. The hardest part of the preparations, in my opinion. This is a slightly more advanced step, but it really helps when you are building a model. When you open a model and it has large white panels to glue together, it is because the designer took the time to build in some convenient panels for the builder. They work great for parts that bulge out and would be hard to attach normally. They also add internal strength to the model, since there is now has a piece of paper holding the sides in the proper positions. Not all models need to be made this way, and we can get away with it for the Attack Bomber, but it's got a great plane in it where a module would help some. So we are going to do it.
Now, look at the model in Metasequoia. Near the back of the model, right where the engine kind of ends, a bunch of faces all line up to make a straight line. It goes all the way around, so this would make a great place to split the model. Other ways to make panels are in good places to split a model due to difficulties in construction. Sometimes you need to pick a place that doesn't have a nice smooth face. My Derelict Heavy Cruiser has a couple non-flat splits in it, but with out them, it would very difficult to make. On the Attack Bomber, if we were to make it so that you glued two separate pieces together right there, it would work great. It would add support to a thin model, and it would make the parts easier to attach. So let's do it.
So, the first thing we want to do is select all the faces that we want to be in a module. Use Select and Normal to pick out the panels we want. Hold down the shift key and click on all the faces that you want to separate. Watch the "F:" number increase each time you click a face to make sure you actually click on it. If you have a hard time getting one, zoom in, rotate, and move the model around until you get it. To check to make sure you got all the panels you want, press Ctrl-H and look for any you missed. Press Ctrl-Z to make them reappear. If you unhide the faces by pressing Ctrl-G you will lose you selection. Just press Ctrl-Z until you get it back if you do that by mistake. Once you get all the faces that you want to include in your module, go up to the Selected menu, and choose "Move faces to a new object." The cyan lines will turn back to magenta and you will have a two separate parts. To check to make sure you did it right, use Select and Joined Face and pick your module. It will be highlighted. If you missed a face or two, press Ctrl-Z until you are back to before you made a new object and get the missing faces. Don't forget to press Shift when selecting more faces.
Making the Connection
Ok, we made the module, but now we need to make the large white pieces that will connect the two. So, select the new object and hide it. You can do this with the Objects Panel by clicking on the eye for the new object, usually called "obj1." This way we will only have the object that we want to attach the faces to visible. Before we make any new faces, we need to select the material we want to attach to them. Since all the existing materials have colors on them, we need to make a new one. Click on the MatPanel button in the System tab on the left. A new little box will appear. Click on the New button and a white box will appear at the bottom of the list. Great, now we have a white material for out modules. Go ahead and close the Material Panel box, since we aren't going to use any other material but white.
Now, rotate the model so you can see the empty bottom. Click on the Create button and then Tri in the Create Face box. Press and hold Ctrl and click on one of the vertices that you want to add a face to. Then click on the second one and you'll see the line turn cyan. Then click on the last one and BING a new face. It should be white and if not, the new material wasn't selected on the Material Panel. You can select the white material and then the Mat button on the left side of the screen and then change the material if you need to. The reason we press Ctrl is to make the new vertex at the same place as the existing one. This connects the faces together and makes for a nice model. Now, keep doing this until you fill up the plane with white triangles. Don't overlap the triangles, since Pepakura doesn't like that, and if you accidentally connect the face to a vertex that you don't want to, just undo it. If you aren't doing a flat surface, remember how you made this side because you will want the other side to match this one.
One, two...
Three!
Finishing the Other Object
Ok, now the original part has a white panel on it. Now we want to do that to the other piece we made. And here's the easy way to do it. Open the Objects Panel and you will get a little box like below. You will see that there the two objects in it. Click on the eyeball next to 'AttackBomber,' and POOF it's gone. Now, click on 'obj1' and POOF the engine is back. Then, click on 'obj1' to highlight it. Now all we have left is the engine part. You can rename it to Engine by clicking 'Prop' and changing the name. This would come in handy for when you have lots of modules and you want to keep track of them. But since we have two, it's not really necessary. I'm just going to leave the name alone. Also, when you have a model already with multiple objects in it, you can use the objects panel to move pieces around.
Object Panel
The bottom by itself
If you don't highlight the correct object, the new panel won't connect to the object you want it to. Also, Pepakura won't connect the pieces together, and everyone will be sad. So make sure you select the part you are working on! If you click off all the eyeballs that you aren't working on, you will know when you have the right part selected. Now, we're going to add the opposite face here. You don't need to make a new material since the white already exists, so you can skip that part. But remember, if you are making a non-flat surface, make sure you make new panels that will fit together correctly. You can see on my Derelict Heavy Cruiser where I messed that up and was too lazy to fix it. Oh well, it works and you won't see the mistake when it's all assembled, so no big deal.
Another tip: Some models have objects that don't have a 'bottom' or are missing a panel, usually turrets or other moving parts. This panel would be hidden in the game since it faces the main part of the ship, but it really doesn't do us much good. So, what we need to do is add faces like above. Just make sure to highlight the part you want to add a back to in the Objects Panel. Otherwise, you'll have separate pieces, and Pepakura doesn't like that too much.
Oh, and a big thanks to Miss Eris Sjet from the Paper Starships Forums! She's the one who hooked me up on how to do the panels right.