The method I like to use when syncing clips with the sync bin is the audio sync but a lot of the time, some clips sync and others don't pick up an audio match.
I would like to manually sync the failed clips using the in/out point and append this sync to the existing audio synced sync bin.
The only way I have been successful in saving manually synched clips is to create a compound clip with the synched video/audio. Then you can just save it wherever you want.