There is no such thing as one is important over the other. They are going to look at it as a whole but, they will only consider the last 2 years of your college. So if you have been in a masters program for 1.5 years and will graduate May 2020, they will consider those 1.5 years of masters grades and 0.5 years from your undergraduate; basically the last semester of your undergraduate. Dont worry about the GPA, because if you have a B in the American system (Which is mostly a 5 level grading system) you get lower quality points which reduces your GPA. But, in the MEXT conversion scale an A and B have the same 3 quality points, so you wont lose GPA here. The only time it might make a difference is when you are being compared to another applicant. If you and another applicant have similar achievement i.e. you published a lot, did good research, both of you have written great research proposals. Then, they are going to look at your GPA, TOEFL, GRE (If applicable for the program).