This is one of the hardest distinctions to make and mostly because the 1E3a is a rare paper on any issue. I have a single 5p1E3a and it is damaged! The 30c1E3a is the least rare, it is printed on bright colors. It is also helpful to know that the 1E3a paper is slightly thinner than the 1E1, but not by much.
For example, the 25c1E1 is a dark pink and very much unlike the 25c1E3a. The 1E1 is cream BEFORE discoloration. If you have a 1E3a that is discolored in such a way as to resemble the 1E1, then it is time to take a look at the color of the stamp. In some cases, you will be stuck with a 1E3a that just looks like a 1E1 or viceversa, but because most 1E3a are not discolored, most of the time there isn't a classification problem.