When you write audio, you write all channels simultaneously, so there's no need to manually set the file position unless you want to overwrite data.
The positioning routines are as follows:
int quicktime_seek_end(quicktime_t *file);
int quicktime_seek_start(quicktime_t *file);
int quicktime_set_audio_position(quicktime_t *file, long sample, int track);
int quicktime_set_video_position(quicktime_t *file, long frame, int track);
The seek_end and seek_start seek all tracks to their ends or starts. The set_position commands seek one track to the desired position. The track parameter for audio is always going to be 0.