You will definitely get used to it (I'm going through the same thing right now with a new bicycle I bought - the seat is new to me so it takes a few rides to build up the tolerance)
You should maybe have a look at our catalog to check out the inflatable seat cushion bottom that we sell. Page 28 - part # 72020028 (you can add it on top of the standard seat bottom, or use it alone - pretty neat accessory!. Here is a link to the catalog section online:
http://www.hobiecat.com/kayaking/accessories.htmlhere is the direct link to the page with the seat bottom:
http://www.hobiecat.com/support/pdfs/ka ... _28-29.pdf