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@kaynala - welcome to MobileRead. What you are looking for is the "Sync from shelf" feature of this plugin, have a dig around in the Help file that comes with it for details.
First you have to decide how you want calibre to visually show books on that shelf - whether it is to have a special tag or a custom column value.
Then go into the configuration for this plugin (authorize the very first time you use it), click Refresh Shelves, choose your "read" shelf and click on the "Edit Sync Actions" button. On this dialog you create what actions you want to take place for each book on your read shelf that you have a matching book for in calibre. Click on the plus button to create your rule(s), setting whatever tag or custom column you decide from the initial decision I said you must make above.
Click ok out of the dialogs, and then on the Goodreads plugin menu you should choose the "Sync from shelf..." option. Choose your read shelf, and then you will be given a list of books on your shelf. Now comes the tricky bit - for each book on your shelf you have to find the matching book in calibre. Thankfully you only ever have to do this once, and if you are lucky it will have figured out some of the matches for you. If you don't have a matching book in calibre, you can create an empty book for it on that dialog (look at the right-click menu)
When you are finished with matching books, click "Sync Now" and at that point every book which you have matched against calibre will have the tag or custom column values applied that you specified earlier in that sync action. Any books you didn't yet match from your shelf will just get ignored, so you can do them at a later date if you want.
Please do read through the Help and then if still stuck ask here. I'm contemplating doing a blog for my calibre plugins with tutorials on how to use some of the more complex ones like this one, but that's nothing more than a passing thought at this point.
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