It depends. To get the most accurate results possible Maps Made Easy uses a Ground Reference image to correct the GPS derived altitude values based on the the SRTM elevation of the ground and the relative altitude as measured from the takeoff location. With a single takeoff location this works great. But, if you are moving around a bunch between takeoffs then this process gets complicated.
If the elevations of the takeoff locations are the same it is not an issue, so do that if you can.
However, if you can't keep the takeoff locations at the same elevation you should not include any ground reference images in your dataset. This will leave the elevation to be processed using the GPS derived tags which can vary 100+ meters between takeoffs even on flat ground.
Since your data is relatively flat I would go ahead and include it. You only need one ground reference image. If more than one are included then the last one the system detects is the one that gets used.