Thomas,
You do not have to calculate the rates for each slice per hand. Using the well bore condition, all the well nodes are internally connected by a 1-dimensional element - like a tube. Thus putting the extraction/injection to just one node (usually the bottom node) and a 0 value to the others the extraction/injection will be distributed to all the slices. The distribution is a result from the simulation, it is not done in advance. Besides the transmissivities of the layers also the head distribution has an influence: If the head is generally higher around the well in one slice, the inflow into the well will be higher, too.
You have probably used the Budget Analyzer to track the flow into the well. This doesn't give you the results you are looking for in case of a multi-layered well. You'll always see the total inflow at the node where you have put the extraction rate, which is due to the fact that the Budget Analyzer only shows boundary fluxes - and the boundary flux indeed occurs at that very node. You cannot use the Budget Analyzer to track internal water fluxes, and the flow within the 1D well element is an internal flow.
The latest version FEFLOW 5.3 contains a new option to calculate the distribution well extraction for each layer as an option in the Fluid Flux Analyzer, which is the tool to calculate internal fluxes. Up to FEFLOW 5.2 there's no such functionality, but if your model doesn't show extreme vertical head gradients you can assume that the extraction is approximately weighted by transmissivity.
Best regards,
Peter