Girlfan, the timelines from the series and the novels are different. Because of the change that they made in the first season, that skipped Kiyoi living with Hira for that period before the confession passed, it has resulted on the characters living together in the second season. The second season would have been unable to adapt the story as it is the novel from the start because of this part that was changed in teh season 1.
What the series did was showing the characters living together at some point in time without showing exactly when it happened. At least in the beginning, because we found out that Hira is now in his four year of college, when is near to graduate. So basically the series has moved the timeline ahead with two years.
Even through the timeline was changed, the production team has done their best to include some of the most memorable and touching scenes from the novel, so they will still be included in the series, even if the timeline is changed. For me is no confusing at all. I think for people who has read the novel, for things to be less confusing, is best to either ignore the time skip that the series has or imagine a combination from the timeline of the novel and the series. In my case, i imagined my own timeline that makes sense.
In my opinion, is very easily to ignore the changing of the timeline in the series because the changes were done in a really clever way. One exemple is how they had Hira and Kiyoi act more comfortable around each other in that first morning in which the characters wake up together at the beginning of ep 1, as if that morning is just one among many others. The way the characters interact suggest that they must have been dating for a while for them to act in the presence on the other as if is a natural way for them to do so.
The changes made to the timeline is indeed because they wanted to cover more of the post-college years, because that is the time where the characters gets the bigger character development.
This change doesn`t makes that much of a difference in my opinion, because no matter how much time those two spend together, the changes they go through are really small, and are not reflected in big gestures, but the small changes in the mindset or subtle gestures. Their relationship doesn`t get stronger and the characters doesn`t change in a short time, is a continuous effort and learning along the way from the mistakes that they make, and this is what makes the novels so amazing.