The SharePoin 2007 integration consists of the parts, one web part and one server side http-handler.
Make sure the MultiFileUpload.ashx is deployd to $SPINSTALLATION\12\TEMPLATE\LAYOUTS\MULTIFILEUPLOAD (the .ashx.file) and MultifileUpload.dll in the GAC.
The Web Part is just to deploy from the bin-folder with the setup.bat script, it will be deployed as a feature to SharePoint. There are two properties to the web part, one "Http-handler url", if you don't change it the default adress will be used.
The other property is "The name of the document library", that is the document library the files being uploaded to.