And should I use repetition allowed, or repetition not allowed formula?
A binary string is a string with 1's and 0's in a row. {0,1} is a different string from {1,0}. Say I'm considering binary strings of length 6 and I want to count the number of strings with 3 1s (and 3 0s). Should this be regarded as a combination or permutation problem? And is this considered to be "repetition allowed?" It seems like it's "repetition required."
You can often solve a counting problem by working out in how many ways you can choose the required object. When doing so, there are a number of questions that are nearly always worth asking yourself.
So, we have to choose $3$ places from $6$, with repetition not allowed and order not important, and the number of ways to do this is $C(6,3)$.