-If you edit or create individual faces you have to always keep order of placing wertices
You see that's why Wings3D rocks,it doesn't create wrong meshes ever,it's technology just doesnt allow it so no prevention is required unlike most modelers which will let you create doubled edges and that's very bad for game design needs
The Doubling of the polygons isn't related to it being converted to double-sided but rather because they were boxes/quads and the exporting via certain format triangulates them.(1 quad= 2 tris)...
I usually use the .ndo export when I assemble different scenes/meshes because it leaves the mesh untriangulated and plus I don't like using 'merge' since I've seen it to be very buggy in most softwares regarding vertex order and transform matrice.
The blue faces are definetely holes...It just needs a few edges deleted/dissolved and maybe some point connects...If you can't get it done,send me the mesh and I'll make a little set of images showing the steps I made to correct it so next time you know what to do.
Sidenote:In Softimage Xsi,when using the 'create polygon' tool and starting a face from the 'wrong side',all you need to do is spin the cursor over the right vertex,without canceling the operation and the normals will change orientation...You can see it from the little arrows surrounding the tool's 'creation guides',very useful and fast,plus you don't have to start over(hence 3dmax's editpoly)...If you still pursue the 'wrong way,Soft. pops a dialogue box to warn you of this irregularity
Modeling Tip of the Week:The more details you put on a model,the more you will learn from it!