Let the interest of 2000 be X%, then the interest of 1000 is (3.24-X)%.

2000 X %+ 1000 *(3.24 X)% = 54.9

1000X=2250

X=2.25

3.24-2.25=0.99

So the annual interest rate of 2000 yuan is 2.25%, and the annual interest rate of 1000 yuan is 0.99%.