I'm not sure that uncrustify can do exactly what you want. You could try to post-process the output with the gcu-lineup-parameters program from GNOME C Utils, which Nautilus already uses for example. The Nautilus source tree contains a run-uncrustify.sh script which does this for each file:
# Aligning prototypes is not working yet, so avoid headers
"$UNCRUSTIFY" -c "$DATA/uncrustify.cfg" --no-backup "$FILE"
"$DATA/lineup-parameters" "$FILE" > "$FILE.temp" && mv "$FILE.temp" "$FILE"
This should work if you only want to process the .c files, but the comment suggests that aligning prototypes in headers is more difficult.