The previous replies are confusing South East winds, with South/East side of the bay.
In a southerly wind any of the bay beaches from St Kilda down towards Frankston are ok, kind of. Just find one that is big and wide with plenty of room and not too many people. Other kiters will be helpful as long as you don't get in the way.
The beaches at the top end of the bay usually have rocks and reefs and groynes to contend with. The beaches from Mentone to Carrum are more sandy with shallower water.
In northerlies your only options are Rosebud and Rye and other beaches down the south end.
sixfiddy said.. ... Had 2 lessons with an instructor and have the kite flying bit down pat, body dragging, relaunching etc. Just need to try work on getting up on the board between lessons. ...
Cheers Steve

You're greatly mistaken if you think you have the "...kite flying bit down pat..." after 2 lessons. The number of lessons is irrelevant. The amount of practice and kiting experience is the important thing.
Kitesurfing is 80% kite skill and it takes several hours of intensive practice to develop the basic muscle memory to be able to do it automatically. The worst thing you can do is jump in the water with your kite and board and expect to be up and riding. Spend much more time body dragging than you think you need to.