Hi Lauren,
This is a known issue when adding Input Datasets one at a time and is currently being tracked here (click 'subscribe' to receive further updates on the issue).
Clicking the reset button to load all the input fields into the Field Map control is a current workaround, as you describe.
As an alternative, you can use the Add Many button to load data from the map and all the fields from the input data sets will be visible.
As an additional alternative, you can browse to the input dataset locations using the folder browse button and multiselect the input datasets.
Sorry for the inconvenience. We have this in our product plan and will hopefully address it in 3.1.