1) the incomplete directory will stay in the same parent level as your download folder.

2) frostwire will not launch magnet links autimatically at this time. you can however, install limewire, setup both to use the same port number, then open frostwire, launch the link, and limewire should forward the link to frostwire. OR you could start the download in limewire and resume it in frostwire. but your having problems with the latter one i see.