One helpful thing I noticed fellow kerbonauts: When taking off, your cargo needs struts in order to stay all nice inside the cargo bays. But if your cargo is another ship that is intended to return to the parent craft in order to land, now what? Well....if it fits snugly on the cargo bay, no problem. It wont clip through after undocking and docking again, which is nice since you can land without the cargo wobbling around, even without struts. Makes sense if you think about how the engine works. You can clip parts when building, and as the cargo is still considered part of the craft when taking off, it is allowed to clip through objects of this same craft. After it undocks, it becomes another entity, which collides with others.