Hello,
You can prescribe the elevation of the number of planes you want: 0, 1, more up to NPLAN-2 planes (the 1st one is for the bottom and the last one for the free surface) as long as they are declared with an inscreasing order. The other(s) can be defined as sigma.
The elevation of plane(s) is to be chosen with a relevant value of your fluid domain (where you will have water and salt). Depending on the reference level with respect to which the bottom elevation is defined (e.g. Chart Datum, Mean Sea Level), the value can be negative or not.
If you need more examples to understand, have a look at the TELEMAC-3D validation document and the associated examples in the validation folder, in particular the user_mesh_transf subroutines in the subfolders user_fortran when available (which means a mesh transformation equal to 2 or 3 is defined).
Hope this helps,
Chi-Tuan