If you extract the files from the hotfix and the README for the hotfix tells you that you need to replace the file ImportantFile.dll which exists in c:\PM
it is just wanting you to go into C:\PM, rename the existing file to something like ImportantFileOLD.dll, then copy the ImportantFile.dll from the hotfix folder into the same directory (C:\PM). At this point, yes, there would be two similar files in the same folder, but only one of them is being used by the product. You'd then repeat that process for how ever many files are included in the hotfix.
If you then decided that you wanted to undo the hotfix installation, you would simply go back into C:\PM and delete ImportantFile.dll and then rename ImportantFileOLD.dll back to just ImportantFile.dll.
Note: You may need to stop the EminentWare Data Grid Service before you go to rename the files and then restart it after the renaming is done.