I know the answer is 6 but I'm not sure the proper method to do it.
How I came to the answer is by shifting two zeroes to the right and count until it reach back to the start.
Starting with 2 zeroes:
0011
1001
1100
0110
Staggered 2 zeroes:
0101
1010
There's nothing wrong with your method, but there's a general formula. You have to choose 2 objects (zeroes) among a total of 4 (the length of the string). That's basically the binomial coefficient $\binom{4}{2}$. So, in general, there are $\binom{n}{k}$ string of lenght $n$ with exactly $k$ zeroes ($0\leq k\leq n$).