Go to Projects on Menu bar ---> Add Source.
A pop-up window will ask you choose the file from a particular directory. After selecting file to add, another window will ask you to 'choose source type' like whether the selected file is a source file, a package, or a testbench. Choose appropriately and then, the file is added to the project. ISE will automatically insert the file within the module as long as the top module is selected correctly.
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