once you design and publish nintex form for a given list it should be automatically used since

Please recall that the OOTB EditForm.aspx was deleted from the list and replaced with a custom list using SharePoint Designer.

So what I had to do so that Nintex Forms would replace the SharePoint Designer customized form was the following:

1. Navigated to an unmodified list in SharePoint Designer in the same Site (You can create a new List if you want to be sure it is unmodified)
2. Opened and copied the EditForm.aspx's contents
3. Navigated back to the list with the missing EditForm.aspx
4. Created a new ASPX page and renamed it EditForm.aspx
5. Opened the file in edit mode and replace all content with the copied content from #2
6. Opened the unmodified NewForm.aspx in edit mode in the same list the EditForm.aspx is being rebuilt
7. Searched for listName and listId and copied the list ID
8. Or go to the List Information section for the affected list and copy the ID from there
   
9. Opened the newly created EditForm.aspx and replaced the id with the correct one
10. Saved the new EditForm.aspx and made it the default for Editing
11. Deleted the SharePoint Designer custom edit form, EditForm_custom.aspx in my case.

Now when I go to the list and open an item in edit mode I get the Nintex edit form instead of the SharePoint Designer edit form.

Hope this helps.