Shane,
In our company we use EPDM liners all the time for ponds. We do not normally use any type of soil on top of the liners that we install because we do not want to add any more organic matter to the water column. We do however like to use a good fabric material underneath to protect against any sharp edges under the liner ie. rocks and such. We have had some great success with these even in the larger pond sizes. I ma not certain on the size that you are looking at but I am certain that it could be accomplished and you would be very happy with the results. \:\)