Hi Kat,
Yes you can start your SeaDoo on the trailer, but don't let it run for more than a few seconds.
You can also hook a hose to it, I made and adapter from a piece of 1/2" hose that I pushed into a 3/4" garden hose, attach the 1/2" hose to the outflow (arrow going out) of the ski. I know this sounds backwards, but it's actually for flushing the ski.
Start the ski first and turn the water on, only about 1/4 turn, only let the ski run for 5mins. or less.
You can also buy a flush kit, but this does the same thing.
If you are confussed, check out the owners manual, you can download it.
Lou