The Layer View in MatterControl will let you preview the print so you can make sure it will turn out how you like.
The print will have all the features of the actual in-game ship, including engines inside of stage fairings and things inside cargo bays.
It won't have the insides of cockpits or the Kerbals themselves, though.
There is a bug in MatterControl 1.3. If your print looks like a giant mess, try turning off Display Extrusions.
Check to make sure that thin parts will actually be printed. If not, you may need to scale up the model more or print it in multiple parts.
If you can't or don't want to scale up the model, the only other thing you can do is edit the mesh for that part in Blender.
Many slicers have trouble generating support structures under the fins. This is because they are thin and pointy on the bottom. You can either try a different slicing engine, or print the fins separately and glue them on.
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