How do I make sure that application does not overlap with the FLASH area of the bootloader?

To make sure that application does not overlap with the FLASH area of the bootloader, you need to change the addresses for m_interrupts and m_text in the CPU build options:

Figure 1. Application Memory Area Settings

Application Memory Area Settings

Note: For the ARM Cortex-M4/0+ you do not need to copy the vector table in the bootloader to a different location, you can debug the application easily without the bootloader.