Hello,
Currently it's not possible to change the link order in IDE (as opposed to e.g. CodeWarrior).
There is a related feature request already logged in our database so this feature might be implemented in a future release.
The only workaround I can think of is to disable makefile generation and adjust the link order manually. See below the workaround instructions:
1) Build the project first - makefiles and .args files are created automatically in the output directory:

2) In the project properties turn off Makefile automatic generation:

3) Change the link order directly in .args file (e.g Startup.o has been moved at the end of the object files):
"./src/main.o"
"./src/intc_sw_handlers.o"
"./src/intc_SW_mode_isr_vectors_MPC5744P.o"
"./src/flashrchw.o"
"./src/Vector.o"
"./src/MPC57xx__Interrupt_Init.o"
"./Project_Settings/Startup_Code/startup.o"
-T
"C:/S32DS_Workspaces/S32DS_PA_1.1_clean/MPC5744P_Interrupt_debug/Project_Settings/Linker_Files/57xx_flash.ld"
-T
"C:/S32DS_Workspaces/S32DS_PA_1.1_clean/MPC5744P_Interrupt_debug/Project_Settings/Linker_Files/libs.ld"
-Wl,-Map,"MPC5744P_Interrupt_debug.map"
-Xlinker
--gc-sections
-mcpu=e200z4
-specs=ewl_c9x.specs
-mhard-float
--sysroot="C:/Freescale/S32_Power_v1.1/S32DS/e200_ewl2"
Note:
If you need to add a source file into your project you should turn on the makefile generation again and rebuild to update your makefile/.args files.
Hope it helps.
Stan