I'm not sure what you mean.
You ask about flags, but I think you are talking about interrupt vectors.
The vectors are indeed at the beginning of the FLASH (or ROM for that matter). Every interrupt source has it's own (or shared) vector. See the specs of your processor for details.
If you use a development board with monitor program, the vectors are usually fixed in this monitor ROM, so you can't change them. The monitor program then gives you the possibility to jump to your own interrupt routine by placing some jmp instructions or jump table somewhere in RAM. Where exactly depends on the monitor program you use.

Happy programming.