@MarkS1, you seem to be all over the place. You certainly might have mentioned in your original post that you had already tried using scenes, although it isn’t clear what your actual problem is, or which problem you want help with, or, for that matter, what kind of help you’re looking for.
First of all, you have to readjust your expectations. SU is a surface modeler. By their nature, all SU models are “hollow.” If you want the appearance of a face to suggest that you have exposed a “solid” inside with a cut, you have to put it there.
Now, as far as your simulation of rising water, who even knows how you did it? It would be hard to agree that there’s a problem with SU when it’s equally likely (or more likely) that something you’re doing or not doing is at fault. The fact is, in your last screen shot, I see what appears to be muddy (or otherwise contaminated) water standing in the pipe. It’s too dark and too transparent to be very visible, but I presume the color and transparency are as you set them.
Let’s try to address your problem(s) systematically. Try to be very clear about what your first problem is, recognizing the difference between you doing something wrong and the program doing something wrong, and try to solve that. Then let’s move to your next problem, and so on.