Does it matter what two factors you select to a factor tree explain?

No. Since you are going to keep factoring until all the factors are prime, it doesn't matter what you start with. Example: 36

You can start with 6 and 6, which you would then break down into 2,3,2,3. You could start with 9 and 4, which you would then break down to 3,3,2,2. Either way, you're going to wind up with two twos and two threes.

2 x 2 x 3 x 3 is the prime factorization for 36.