As you know, you can cut your xs at any scale you choose. The xs sheet layout tool will ask you for a Horizontal and Vertical scale, these defined horizontal and vertical scales need not be the same as the horizontal and vertical scales at which the cross sections were originally created, but they cannot be a distorted scale. ie if you cut your xs at 10:1 you cannot layout at 20:1. you could, however, maintain the ratio and do 20:2...
the sheet cell should be at scale 1, so that the program can scale it as needed. the actual dimensions will be multiplied by the scale.
your D size sheets and scale is a microstation plot menu function. nothing to do with your xs. once you produce the xs sheets at the desired size, you worry about the plot scales and how they come up on paper.
this is not exact science and there is a lot of trial and error involved. the good news is that once you have the right sizes and dimensions, you are set for ever.
most DOT's have standards and have figured out what works for them. You should look into someone elses layouts and try an modify them to fit yours.