So for example,
13 in binary is: 00000000 00000000 00000000 00001101. Would -13 be stored as 10000000 00000000 00000000 00001101 (using the most significant bit to represent the sign) or would it be stored using the two's complement? (Specifically in C)
If it is stored using the most significant bit to represent the sign, when is two's complement actually used?
C may store negative number in any format depending on the implementation. The most popular (nowadays other systems are almost not in use) is two compliment format.
But your numbers are not 2compliment ones.
-13 in binary is 0b11111111111111111111111111110011
to see the unsigned representation of the negative numbers: https://godbolt.org/z/ajDDvc