Hey,
the way to specify a well in FeFlow is to assign type 4 BC's at nodes that fall within your filter (screened segment) of your well. Don't set BC's, where the well is cased.
We typically set the pumping rate at the bottom node, and 0 at all other adjacent nodes as you suggested in your posting. That way, if the upper nodes of the well start to fall dry due to the pumping, the BC value is still specified at a saturated node. Whether that is necessary for the calculations to be correct, I'm not sure, but it just adds a little bit of peace of mind. The actual pumping from the different layers along the filter will be determined during the flow simulation and is based on the transmissivities (as far as I know).
Hope that helps, Chris.