I am also going to lodge application to ACS by nxt week for skill assessment.Iam also a Software engineer with 5 years of experiance. As an advice i can tell you that, you have to upload all your Exp.certificate in pdf formats. Since your experience and qualification is accessed by ACS as per instruction given by Aus.immigrn dept. u will get points based on your experience r8? During EOI submission u will have to provide Exp. details as well as assessing authority details. So i think ur qualification an exp. details will be cross checked with ACS.
In which visa category are you trying ? Through agency or self?