Hmm, well I DID do IB, and while I didn't do a science EE, most of my year did, and what they were told was they should structure it largely as a "large IA". So...hard to say :s
However that was a few years ago, so the rubric for EEs may have changed. I believe the IB has a big book which covers every subject possible in the IBD and has notes on how an EE in each subject should be done with the rubric (e.g. Economics must have primary data - or at least they used to require it). See if your IB coordinator can find out the format for your subject.
Beyond that in sort of general academic settings the presentation of something like that as in e.g. a dissertation, thesis, journal article etc does have some similarities to how you might structure an IA lab report, but some differences. This will probably vary a bit depending on subject, so I'd recommend looking around at "scientific academic writing" resources on the web, or something along those lines (I imagine there are a few).
Broadly speaking generally it would be something like introduction (inc. background and literature review), methodology (i.e. experimental set up - so someone else could read this and set up and do the same experiment/work), results, analysis of results, evaluation of results (i.e. what limitations there are, how the work could be reasonably extended/improved with more time/money/facilities and specifically, what), and a conclusion (which is normally written under the assumption someone reading your paper is going to read the abstract then the conclusion and probably not much else). This is however conjecture, and there may well be more specific formatting requirements for IB EEs - these would obviously supersede the above.