MapObjects 2.0 will project from WGS84 to AGD66 on-the-fly. To do this you need to:
1. Create a new ProjCoordSys object, and set it's Type property to the constant moProjCS_AGD1966AMG_55.
2. Set the CoordinateSystem property of the Map object to the projected coordinate system you just created.
3. Create a new GeoCoordSys object, and set it's Type property to the constant moGeoCS_WGS1984.
4. Set the CoordinateSystem property of the MapLayer to the GeoCoordSys object you just created.
5. Create a new GeoTransformation object, set it's Type property to moGeoTransformation_AGD1966_To_WGS1984, and it's Direction property to moDirection_Reverse (to shift from WGS1984 to AGD66).
6. Set the GeoTransformation property of the MapLayer to the newly created GeoTransformation object.
Note that steps 5 and 6 are necessary because there is a datum shift between AGD1966 and WGS1984. If you don't do the datum shift, your WGS1984 features will appear to be shifted by around 115 metres from where you expect them to be.
As for determining the coordinate system for data, it's a little tricky. I suggest you read the on-line help which has a lot of useful information and techniques.