If you save your documents as layered file you can reopen the saved document file back into Photoshop as a layered document and replace layers that makeup footers headers etc.  Templates are different more or less a model of what you want to make.  You model your design in a  template with or without some content. You model|reserve space for the content you want to add latter.  The Way template are used is you open one of your templates. Then you populate the template with you want it to content then you save the populated template under a new name that reflects the populated contents.  For example a Baseball Card populated with a player may be save as the babe.

Template examples can be found in my Photo Collage Toolkit Documentation and Examples

In a single document you can have several pages and these pages may have headers and footers that share smart objects.  If you replace the contents of the an embedded smart object on one page page that is shared on an other page the pages you will see both pages contents are changed. For they share the common object.   It is also possibly to have independent smart object layers. It depends how you create the layers in the single document.

Example one sharing a smart object hi-light a smart object layer and use menu layer>Duplicate Layer... This will create a second smart object layer that share a common smart object. Each layer has is own associated transform. Do it again and you will have three layers the share a common smart object. So you can use each layer associated transform to position and size the layers contents. Make a picture package for example. When you hi-light any of the three smart layers and you use menu Layer>Smart Objects>Replace Contents... all three layers contents will be replace with the new smart object.  Care must be taken to replace the smart object with an identical size object for only the object is replaced the three associated transform for the three layers are not replaced or changed.

Example two independent smart objects  hi-light a smart object layer and use menu layer>Smart Objects>New Smart Object via Copy.  This will  create a second smart object layer that has it own embedded smart object copy.  Do it again and you will have three all have independent embedded smart object that are identical.  However they do not have to remain identical.  For example if the first smart object layer was created by using ACR to open a RAW file as a smart object layer the embedded object is a copy of the raw file and its associated RAW conversion settings.  Double clicking on one of the smart object layers and you will see ACR open on its embedded RAW file with the embedded RAW conversion setting.  Changing these settings will update the layer smart object content with new ACR setting and pixel when you click OK in ACR. Repeat for the third and you will find you have three different raw conversions in Photoshop you can mask and blend together to bring out detail.

I think what your missing is that a smart object contains a copy of the original object.  Changing the original after creating a smart object layer in document will not effect the smart object layer at all. Its independant from the original having a copy of the original. Only changes to the smart object layer and its embedded smart object effect smart object layers.

I usually do web page variations with layers in one file using the Layer Comps. If you are not familiar learn about Layer Comps and see if this helps.