Is possible.
However, Synplicity recommends setting the constraints in the Synplify software and passing the constraints to the Quartus II software using a Tcl script for best results.
For performance considerations, calling Synplify from within the Quartus II software is not recommended.

For details, refer to the Quartus II Handbook at the URL link below and search for the keyword “Using the Quartus II Software to Run the Synplify Software”.
  https://www.altera.co.jp/ja_JP/pdfs/literature/hb/qts/quartusii_handbook.pdf

For the settings to use the NativeLink function, refer to Elsena document: Quartus II Getting Started Guide - EDA Tool Settings.