Oh, actually it's the same exact class, so my question is really how to set up a bundle with two AUs in it.
Looks like I have to keep using the .r file for compatibility with Ableton Live (possibly others). I tried two .r files (effect and instrument) but that only produced one AU. My .r file looks like:
#include <AudioUnit/AudioUnit.r>
#include "AudulusAUVersion.h"
// Note that resource IDs must be spaced 2 apart for the 'STR ' name and description
#define kAudioUnitResID_Audulus 1000
#define RES_ID kAudioUnitResID_Audulus
#define COMP_TYPE kAudioUnitType_MusicDevice
#define COMP_SUBTYPE Audulus_COMP_SUBTYPE
#define COMP_MANUF Audulus_COMP_MANF
#define VERSION kAudulusAUVersion
#define NAME "Audulus: Audulus"
#define DESCRIPTION "Audulus"
#define ENTRY_POINT "AntimatterAUEntry"
#include "AUResources.r"