If you are certain and/or have documents like cemetery records that there is a burial in that place, here are a couple of ways to do this:
1. Some people just put a group of flowers or a rock at the place foot/head and photograph that, then transcribe it as the grave with all known information about that person.
2. Some people carry large felt-tip markers and make a temporary sign that they photograph on top of the grave location. Then during transcription they add the details of names and dates as much as they information for.
If the unmarked grave is adjacent to a marked grave, it can be linked to that marked grave to show its approximate location. If the marked grave is not a known relative, be sure to include that information in the "Grave Information" section, so future users will know that are not related.
An overview photo showing that "empty plot" in relation to several others is also helpful. It may be that a future person will decide to place a permanent stone there is they are sure that is the burial place.
If you do not know the identity of the person but you are sure it is a burial (sunken grave, missing information on the funeral home marker, etc) go ahead and photo it and transcribe it as "Unknown Unknown". Don't leave the name fields blank.
Reply back here if you need further help with this issue.