Hi Majith,
With your passport number, dob, and your previous application number CHC will always track the information you had provided in your last information including your BE education details.
I understand and agree with your concern. You best bet would be to highlight your arena multimedia education, and still show that you have a solid background by showing your BE credential. Please also provide a strong SOP with your application stating your interest and previous background in animation.
I believe you are talking about the third page of IMM1294E in which there is only one column for post secondary education. Technically speaking, your BE is a college degree and Arena Multimedia is a certificate course so you should fill BE. However, this is 'my' opinion and I'm not a Visa expert so you might want to consult it with others as well.
If you are providing your resume, you should mention your education/work done in animation area in that as well.
I think you should have a good chance to get visa if you highlight the animation part in your education. Somebody said in another thread that you can file under SPP again (even if you have received a rejection). I cannot deny or accept this fact but you might want to check with a visa consultant for that.
GS