To tackle the Harvested crop location issue, you can go to Accounting - Inventory Maintenance and select Move Harvested Crops. Select the correct Year Commodity from drop down list. In the From Location drop down will be all your field names as storage locations. Select the first field name. From the To location you can select any storage location. Enter qty amount to move, enter desired date and click Record. Example if some fields were placed in a ON Farm Storage Bin and other fields were hauled to Terminal/Elevator all those storage locations can be setup under the Resource Menu - New Structure. Doesn't matter if you own the structure or not. This would have to be done ahead of time so when using the Move harvested crops all those choices will be in the drop down.
When reading in as applied data (planting - fertilizer or chemical applications logged with FMX do import one file at a time now, if on a current version. However, the reason the Yield data cannot be imported one file at a time, is because you have 2 folders. One called AgGPS where the calibrate files are saved and the Task Data folder where the yield raw data has been saved. It takes both files to get the most accurate yield data to read into FW. Most other yield monitors or console, save all files in one folder.