Structure ID is what connects organization and position structures into an inseparable pair. An employee can be assigned to multiple organization units with multiple positions, but a unit and a position have to share the common structure ID.
In case of a companies, it does not matter if you start with creation of a position structure or an organization structure, as their ID is generated when a company is created. In case of matrix structures, however, you need to create a structure ID to define a position structure.
The matrix structure identifier is automatically created when a matrix organization structure is defined. It has the same name as the topmost organization unit (the root) of the matrix organization structure. Therefore, to define a matrix position structure you need to at least create the root of a matrix organization during the Define Organization Structure process.