So I'm doing measurement problems using the factor label method, but I'm confused as to when I'm supposed to put the answers in scientific notation.
I'm not too sure what you mean by the factor-label method but if it's similar to dimensional analysis then using scientific notation should not matter - it would depend on what your teacher wants. Personally I prefer to use scientific notation for anything with an exponent of -3 or 3 (for example $\displaystyle 1034 = 1.034 \times 10^3$)