Hi Chris,
Unfortunately the software modules require fairly specific placement of high performance code, so are a bit beyond the scope of the New Project Wizard.
Where possible, use the project options to configure things like heap/stack placement, external memory partitioning, etc. However, when it comes to adding customizations like adding INPUT_SECTIONS commands the only option is to do it manually, and make sure you do it within a generated $VDSG section. The tools that refresh/regenerate the LDF and Startup Code (based on changes to the project options) leave the $VDSG sections intact, including any customizations you make.
Regards,
Craig.