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90 acres isn't that big and can easily be covered in a single map as long as you aren't flying super low. It may take a couple of flights to collect the data but it can all be processed together as long as it is all collected in one shot. Breaking multiple flights up over different site visits will give different lighting conditions and cause feature matching issues.
Maps Made Easy will accept up to 4000 images at a time but generally it is best to limit that to 1000 images until you are really solid on your data collection.