I'm fairly new to working with ArcGIS Online and I have a few questions. I'm a summer intern at a state agency and my duty is to produce a catalogue of contaminated properties in several counties in my state. I am creating this catalogue in ArcGIS Desktop, but the end product needs to be published on ArcGIS Online. As a college student, I am accustomed to working in ArcGIS desktop with shapefiles in my classes. So far, I am working with shapefiles for the state counties (polygons) and shapefiles of the various types of contamination (points). I have noticed that many types of data that are available from ArcGIS Online (as well as other data websites) are in layer format, not shapefile (such as state hydrological data). Is it fine to work with feature layer files instead of shapefiles? I have looked this up and I'm not finding a clear answer about the difference. My second question is about the interaction between ArcGIS Desktop and ArcGIS Online. How should I transition my final product from the desktop setting to the online setting? I know that ArcGIS Online uses base maps, but my project so far has been based on the geographies I downloaded from the Census Bureau (TIGER/Line).
I realize that my questions are probably rudimentary. I'm still learning the basics of GIS. Thank you for any help.