1) You can use the LISTPATH directive to set a different location for the Listing directory. This will then override the directory named 'Listing' where the list files will be put by default if you just click the 'Generate Listing File' checkbox.
The LISTPATH directive takes a path name, either relative or absolute to the directory you want the listing files ot be placed in.
2) The USE(configname.cfg) directive will tell the checker which directives file to use for additional directives. This can obviously be a relative or absolute path.
When working with remote projects you have to remember that while the compilation will be occuring on the remote machine, any background parsing in the editor will be occuring on the local Windows machine. This means that any files referenced in the USE directive on the remote Linux/Unix won't be found from the Windows machine.
Ideally, any directives would be added into the respective 'additional directives' boxes where the IDEs know about them and we can correctly call the compiler on both the LInux and WIndows platforms.