Bummer, sorry to hear about your experience. The water could have got in one of two ways, the transom plugs or the drive shaft seal(s). Transom plugs are easy to fix and/or replace, usually a simple rubber o-ring. The drive shaft seals are a bit more work. Did you notice any cavitation (engines rev. but not quite going anywhere) while on your first ride?
In any event it is critical that you get the water out of the engines ASAP if any was ingested. Not sure if you or your shop will do this, but if there is water in the crank case or cylinders it can ruin the engines in as little as 24 hrs by rusting internally. Need to crank the engine with the spark plugs out to purge any water, do a couple oil changes, then try to get them started and up to temperature to evaporate any residual water.
Once you get everything running it would be a good idea to go through each and every electrical connection that could have been under water and make sure it is dry and lubricated with dielectric grease. Things can corrode quickly (especially in salt water) and you could start having all kinds of electrical gremlins...
Since you are new to seadoo's, do you know about the superchargers and issues related to those? If not you need to seriously look into getting those rebuilt before taking the boat out again. If previous owner cannot provide evidence of a rebuild in the last 100hrs of use or 2-years then they need to be pulled and rebuilt. Neglected superchargers will explode in the engine and destroy it. Search the threads for more info about this.
Hopefully everything gets corrected without too much trouble and you can get out on the water to enjoy the rest of summer.