as for the question of where remote files are placed, have a look at page 5 of this thread.

"1. sudo gainroot (rootsh needs to be installed)
2. cd /home/user/MyDocs/qtirreco/Remotes
3. rm <remote file name>
4. vi remotes.conf
5. press a for example in vi editor, select the line which contains that remote name and press d to delete that line, then set current remote in line one existing remote. Press ESC and type :wq to save changes."

the remote files created by Winlirc should be compatible with qtirecco (assuming no more changes to winlirc's file formats since the project has now found a new maintainer). i'm guessing he won't break compatibility since there are already a ton of remote files published on http://lirc.sourceforge.net/remotes/

wish me luck