Well first welcome to the website! Congrats on your new baby and we all hope you have lots of fun with her!
Now for the question in hand.........What year, engine and outdrive system do you have and is it a closed colling system? If you are going to tell me a 5.7 and with alpha or bravo drive that would be about right. Now if you have a bravo drive your impellar is in the engine compartment and if you have a alpha drive the impellar is on the lower unit. Whatever the case the impellar should be looked to make sure it is in good condition. The closed cooling system is like a radiator in a car only in a boat, you have a heat exchanger that like a 4 foot round piece of salami. If you have one of these they need to be flushed also.
I'm going to guess and what you saw is the water inlet for your head-toliet (hope you have one) or do you have A/C? That would be what you saw about a 1/3 up from the stern on the your hull bottom.
To flush your engine with fresh water get a medium stream of water going through the ear puffs and place the ear puff on the lower part of the outdrive from the front to back end of the drive over your water pick-up vents. Don't worry if you have water leaking all over the place that is normal. Keep the water preasure down to medium.
Then let the water run for a few minutes and then start your engine up. Watch the temp guage and when the that gets about 160 or so/or levels off, you know everything is open and let the engine run for a couple more minutes. Shut the engine off first, then turn your water off and your done. If your in salt water all the time general maintence on your risers and manifolds are about every 5 or 6 years replacing them.
There are a bunch of flush systems that you attach to your engine that makes this process real easy, but are very pricey! For the most part you take a garden hose connection and snap it on to a another connection turn the water on flush and your done.They can extend the life of your engine in salt water.
I know others will chime in here to help if you have more questions or if have totally confused the youknowwhat out of you( Not my intentions)
Good luck with your new baby and Happy Thankgiving