Yes, you're wrong somewhere. var a = new Array(3,3);means the same as var a = [3,3];. It again creates an array with two members: a number 3and a number 3.
Array constructor is one of the worst parts of JavaScript design. Given a single value, it determines the length of the array. Given several values, it uses them to initialize the array.
Always use the syntax var a = [];. It is consistent (as well as shorter and easier to read).
. .
var a = [
[1,2,3],
[4,5,6],
[7,8,9]
];