Increasing Relative Altitude Accuracy

Hello, I am still learning so please forgive any ignorance on the subject.

 

Long story short, I am attempting to obtain fill volume measurements empty pits to be later filled with water.

 

We have taken scans of several of these pits and I continue to run into the issue of there appearing to be a several foot elevation difference between opposite corners of the pits. The images I am attaching show only a ~2ft difference but more often than not I get results showing an 8-10ft difference between corners (which makes it appear that one corner of the pit would overflow before the rest), so this one of the better results that I have gotten.

In actuality these pits are level and not built on a downhill slope of any kind so I know this elevation difference is an error. 

How can I increase the accuracy of the elevations/altitudes across a wide area? I understand that GCPs or MTPs are probably going to be my answer, but I am unsure of the best way to go about using this feature. Do I need to just paint some boards to place in the project area for me to later mark on the GCP/MTP Basic Editor, or do I need to invest in a survey-grade GPS tool to be able to obtain accurate xyz coordinates to place into pix4d? Or are there some other settings I can tweak in the mission planner app (such as increasing my overlap) to obtain more accurate results?

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