Does myWMS LOS support partially filled palettes?

Yes it does.
You are even able to put items on a already stored palette in case that it is not full
There are no constraints that permit this (see unit load)

How is the warehouse topology entered to the myWMS LOS?

This is done by importing an XML file (menu: File -> Import). See UserGuideDataImport for more details. At the moment we are developing a module to design the topology (racks + storage locations) graphically. But I can't tell when we have a first release and if it will be released under the GPL.