We typically recommend to use Hot Jobs as a way to track Punch List items. By marking the job as Hot you now have a central place to track all Discrepancies to be completed.
From any grid within e-manage you can right click on the project → Actions → Mark as Hot Job → Supply a Reason Why → and OK.
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You can always select the Actions menu from directly within the Project as well. Additionally, if you are a Cloud user and have access to the e-manage|ONE GO App there is automation built-in that will automatically mark your Project as a Hot Job. See here for additional information about how to properly handle Punch List: Punch List
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Once the job is complete and the customer is fully satisfied, ideally the paperwork from the Punch comes back marked as complete, your scheduler or project manager would mark the Implementation as complete (see Completing an Installation for additional details) and then un-mark the job as a Hot Job by right clicking or using the Actions menu to "Undo Mark as Hot Job".
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Again, see here to take full advantage of Punch List Management: Punch List