I am not quite sure what the problem is.
"Tools" probably refers to the toolbar which has a short cut button to start the autonumbering wizard. Move the mouse over the toolbar until it shows a corresponding bubble help.
Track numbers will not be copied automatically anywhere.
If you want to rename a file so that the name features tags or parts of them, use the Converter > Tag - Filename.
For this converter you have to enter a mask which consists of tag-variables (and/or text).
A right-arrow in the dialogue helps you to compose a mask from variables.
A fairly often used mask would be:
%track% - %title%
If you want to have leading zeros in the filename, use a mask like:
$num(%track%,3) - %title%