So I had a similar question and I called Optomcas. Basically, what the person told me was that you should finish your regular application, then finish the essays and then under "School Designations" you should fill out all of that information they ask. If the school designation asks you for an essay with the same prompt, you should be able to see a pull down menu where you can choose the essay you wrote on the main application page (your PS). Im assuming the "secondary" applications youre talking about are the ones under School Designation. If so, finish them before you esubmit.
You should esubmit when there is essentially nothing left that is in your control. So when transcripts get processed, and when professors write the LOR's are not in your control. But as far as essays and questions go, you should fill them out before hand. You can definitely call to re-confirm anything I just said, but this was what i got out of my conversation with an optomcas representative.