Tracking pupil progress is a really important job for HoDs and all science teachers. I have been contacted by Science Monitor who are offering a 20% discount on their monitoring software. I do not endorse this product but you may wish to visit their web site to see whether it might help you track pupil progress accross both keystages. A link to a free evaluation download is included below.
Science Monitor can store all of your pupil marks and information, and then analyse data for departmental analysis. Science Monitor has been extensively updated to support the new GCSEs from all of the major exam boards (AQA, EDEXCEL, OCR & WJEC) and now also allows import of data from any source to any field within the program. More details can be found on the Science Monitor website at www.sciencemonitor.co.uk
If you have not had time to evaluate the software, or need to order a new demonstration copy, then please download the evaluation version from http://www.scimonsoftware.com/download.htm