Thanks for all the replies.
When I signed up with them nobody mentioned about having to use the portal that vortigern linked to, but they did get all excited about the E-cert software. When using the E-cert software you have to choose a status before saving the form, the choices being 1) incomplete 2) complete 3) submitted. I assumed that by clicking submitted that I was submitting to building control, similar to the way that Elecsa do it (who I moved from). If not who am I submitting it to, I fear the answer may be that great god idontgiveashit
The whole notification process is a bit of a cock-up to be honest. Early last year I attended a property rewired by a Polish crew and discovered unprotected meter tails that were concealed and well in excess of 20m. A quick call to building control and I was informed that the council were unable to access notifications received prior to 2013!!
When I enrolled with Stroma I was told that I would be able to do third party certifications as I hold the 2391 and this would be enabled after my first assessment with them (which is overdue) and I understood to be merely a matter of them enabling access to a new form on their E-cert software (they control the forms that you have access to, we don't all have access to the same forms).
When doing the course for the 2391 a similar question was asked and we were advised that there would be nothing to stop us doing a single circuit (orcovering only as much as required) EICR as long as we were very specific in the extent and limitations section