Version 4.4 will include the new Farm Site Mobile program. This program will allow you to map out field boundaries and record soil sampling on a laptop computer that is hooked up to a GPS receiver.
With regards to using different legends, you can use different legends for different layers. This means that as long as you are putting each yield map (probably each field) on a separate layer, you will be able to use different legends. Additionally, you will be able to have more than one available legend for each layer (however you can only use one at a time).
With regards to relating yields to variable rate treatment, Farm Site includes a feature that allows you to show the average of any data (such as yields) based on areas on another layer. To do this you will need a layer for the variable rate treatment that shows the different areas that were treated differently. You can then select all the areas on this layer (with the Pointer tool) and right-click and select Average Polygons. You will then select the layer that you want to average (in this case your yield map layer). The result will be that you will have a view of your yield data that will show the average yield for each area that you treated differently.