I have a 2001 3300scr. with the same problem. There was a thread about this when i checked a year ago and there were two main solutions:
1. make legs for the seat
2. place a cooler underneath the seat for added support.
I did the cooler trick. it works ok. I was going to make a box to put under the seat but in my boat it would have to be removable to access the port engine.
Hope that helps.