Eliminate the need to duplicate files across site collections.
Whether your SharePoint site uses one site collection or many, there are ways to make your design and development more efficient. See below for some best practices I've developed.
It's good practice to work under the practice of one file, one location where possible. SharePoint tends to treat site collections as silos, and that can be nightmare for a designers. To match look and feel across multiple site collections you have to perform the same action multiple times. Typically that means duplicating files and data. Therefore, whenever you create a file that may be used across multiple site collections, it is best to save them in one place and work from the same file. That will means changes are reflected immediately across all site collections.
I recommend using a library in the root site collection as your global location. I just use one library and break it up by file type using folders (see below).
Using this method I can share icons, scripts, and mini apps across several site collections.
This opens your library and all its files in a Windows Explorer window.
At this point you're able to open your files with you editing program, and upon save the file will automatically be updated to the SharePoint library. In addition, if you create a new file and overwrite any file in the library, it will be reflected in SharePoint.