Combining Complex Models I am very new to blender, and I have created a complex spaceship with multiple turrets that are parented to swivel on the correct axis. I want to be able to combine the entire thing under one file so that I can easily sort and animate it in a fleet formation. So far the only way I can find is to join all parts together, but this leaves me unable to move the turrets. As seen in the picture, the parts add up fast, yet I can't seem to find a way to join them into a 'folder' I guess so that I easily access other ships without having to sift through all of the duplicates parts
Parenting is hierarchical .. so  depending on which parts of your model you want to control other parts, a object can have siblings and a parent, and its parent can have a parent of its own.. and so on. The 'family tree' is normally collapsed in the Outliner, reducing clutter. You can select multiple objects and parent them to the last selected (active) object simultaneously, using Ctrl P.

You could join all the objects you don't want to move independently, and make the turrets children of the joined object. (The turrets' children will become grandchildren of the joined object)

Or, create a heirarchy of parts. In it, you can make a link between any child and its parent 'rigid' with respect to translation, rotation, and/or scale by locking the child's own transformations using the padlocks in the 'Transform' panel of the Properties Region of the 3D View. This will mean only ancestors can move the  children in those ways. If you want to lock multiple children at once, select them, and hold Alt while locking.