Hi Bojana,
I'm still not entirely sure I understand what you are trying to do here. You could link the programs to different addresses (say prog1 at 0x8000, prog2 at 0x9000). Then have a third assembly level program that tests a flag (at say 0x1000), and then based on that, jump to appropriate address. Note the thumb code address should be "odd" in the below as least significant bit highlights to the core that you are going to Thumb state (even though Cortex-M3 only supports Thumb state...).
AREA test, CODE
ENTRY
flag EQU 0x1000
prog1 EQU 0x8000 +1
prog2 EQU 0x9000 +1
testflag
LDR r0, =flag
LDR r1, [r0]
CMP r1, #0
LDREQ pc, =prog1
LDRNE pc, =prog2
END
