The lowest spot should be right under the step inside the cabin.... just lift the lid and take a peek.
As to the drains: There should be a valve on the line leading from the sink drain so that you can shut that line off to prevent water from filling the boat if something else plugs, or if that drain goes lower than the surface of the water when heeled. I've also seen a valve on the lower portion of the "Y" to keep the scuppers from making a "woop" sound while underway.
Since the scupper tubing has a small inside diameter, it can and will plug easily. I keep a small piece of wire handy for unplugging, and I like to blow them out on occasion. The screens help keep gunk out of the lines. If you have access, a turkey baster jammed into the scupper tubes works well to blow them out.