I would do each general area individually and process it as probably 5 or 6 different maps. Any single map you run on Maps Made Easy has to be contiguous. You can't have islands of data that aren't connected with adjacent data.
For example, I would plan a mission to cover all of that northern section as one. Then collect the data all in one visit and process it together. Use 75% overlap since there are minimal tree blocks and you are flying pretty high.