Hey guys i have a 2009 sunsation SSR with twin 496's and when the boat is running it beeps two times slow every 5 mins or so does anyone know what this is??

Could be a lot of things, check out this thread:

mercruiser 496 engine alarm sounds - Speedwake 2.0

Check for codes. If there is one, it will lead you to the failed part. If there is not one, then check idle counts. If they are stuck on 99 you have a bad idle air control, very common. Do not keep running it like that or it can damage the computer.