Specify include path in Quartus II
Altera recommends that you use the SEARCH_PATH assignment to define
  the project libraries. You can have multiple SEARCH_PATH assignments.
  However, you can specify only one source directory for each
  SEARCH_PATH assignment.


For example:

set_global_assignment -name SEARCH_PATH "../other_dir/library1"
set_global_assignment -name SEARCH_PATH "../other_dir/library2"
set_global_assignment -name SEARCH_PATH "../other_dir/library3"


Please refer to Managing Quartus II Projects document for more details.