Put the car back together yesterday with my now dry underlay. The towels I had used as a temporary replacement were bone dry after a week of being in there so the butyl seal is doing its job.
Such a good feeling to know all is sorted now and that the job has been done properly.
Many thanks to all for the help in this thread!
If the pictures on page 1 don't work, follow this guide
http://dubsteve68.blogspot.co.uk/2011/05/seat-leon-leaky-door-seals-repair-guide.html?m=1
Just come some vs in the rubber seal on bottom of your doors I did this 2 months ago had no problem since