1) The Incomplete directory is always located where the saving directory is. If you change the location of the Shared folder, your Incomplete folder will also move to the same parent directory.

2) Newly downloaded files are added to the library automatically. If you just move around some files with another file manager, LimeWire will not keep track of it. If you click the refresh button and files do not appear that may either be a bug (one that I haven't heard of before) or the files that do not appear have a file extension unknown to limewire. To add other extensions to the list of shared extensions go to tools->options->sharing.