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First off, you can rename the occurrences in your assembly in the Model browser, this won't affect the part number or file name of that occurrence, this way you can give each a unique name in your iAssembly table.
After naming each occurrence what you want edit your table by double-clicking the Include/Exclude feature under each part located under the Components tab:
Also when you right click the main Table node near the top of the model browser you'll get an Edit via Spreadsheet option. This will allow you to edit the table in an Excel like environment including Find/Replace, mass copy/paste, etc.
They last thing I should mention is iParts and iAssemblies weren't really meant for template manipulation, they're really more for creating the libraries for your top level assembly template, using iLogic to edit your iPart/iAssembly tables is not recommended.
Basically the recommended route is use iParts/iAssemblies to create your libraries and then use iLogic at the top level to create your template.