It appears you have done a lot of work without a basic understanding of grades. Using that red cup for scale, I'm going to assume that the top level is at least 6 inches above the bottom surface. The standard formula for grades is 100 inches of run will equal a 1% grade. 50 inches will be a 2% grade, and 25 inches wil be about a 4% grade. A 2% grade is considered a moderate railroad grade and 4% is a steep grade.
Let's assume you will be forced to uses a 4% grade because of your limited space. 6 inches of rise x 25 feet means your spur to reach the upper track will need to about 150 inches long, or about 12.5 feet. That means your track to reach the upper grade will have to be flat at least 12.5 feet from the start of you grade and it then must rise the six inches while traveling 12.5 feet. This doesn't count any grade transistions, which will make the real number about 14 feet. Since most of that 14 feet will be on a curve, your effective grade will be more like 5%, which means maybe a regular locomotive and one or two cars will make it up the grade. Getting things down the grade will be a real nail biter also.
Any idea on how you're going to find space for that much track on a layout your size? A helix could do it if you wanted have the entire inside of your layout to look like a stretched out roller coaster.
You need to rethink the whole concept of an upper level.