hi there ponderosa, you really do need to make sure rain doesnt get down into the preform, especially considering how much rain we get here in cumbria ! ime in whitehaven myself, the safest bet would be to raise the preform ! if the decking was fitted corrrectlt it should only be screwed down and wouldnt take much work to lift a few boards and reinstall once pond is sorted, if you really dont want to do that then you need to make sure no runoff is going to get in, maybe a barrier from the outside of the preform over the sand bag and then the pond liner over the top, as for the shallow end the sand bags definatly need to be under the liner,
oh and welcome to the forum
ps i know you said the small koi was taken by birds but them with 10 goldies is a lot of fish for a small size pond like yours, my pond is 10ft x 8 ft and i only have 10 goldies/shubunkins/comets, in there !