I don't know what kind of software you used for this game, but I can definitely tell it's very much not designed for it. It seems to be RPG software, but that really does not work well for visual novels. Might I suggest Ren'Py instead? You do say it's a Visual Novel/RPG hybrid, but so far I haven't seen any RPG content. The engine doesn't allow saves in VN mode, so I'm assuming you actually need to get through the *entire* VN portion to save in an RPG section -- but I don't have the slightest clue how far in that would be.
I'm glad you brought this topic up, After Dark is designed to save automatically at the end of each day, this is to help ensure your actions and decisions have consequences, some come into effect sooner rather than later. Given only day 1 is available at the moment we haven't seen this action as yet, but rest assured with the next few days release, you will see it often.