This is meant for both runs but I can't help with some of the confusion. I'll explain later, for the good run in the decision is mostly golden sword you'll choose. But for the bad run, just choose the azure sword instead. You will have to do this process a couple times. The final opponent in both runs is Groh with infinite soul charge.
One key thing I noticed to see if you are going for either ending is the color of your aura. If your aura is bright whitish blue, you are mostly on the good run path. But if your aura is a purplish red instead, you're going towards an evil run path. There's five chapters you need to play through. Earlier I said I can't help much with the confusion.
The best way to describe it is sometimes the story. Which uses an open book icon doesn't always appear. Sometimes, it's on another location. Sometimes, it is one of many objectives you can do it for that area. Usually, later on if this happens that story icon isn't going to be the first thing to pop up there. Luckily, you can use an option to move around the map.
More directly, the traveling option where you can high light any icon to see what's there. Sometimes, you need to do one of those objectives you wouldn't think would lead to an actual story portion. This may take some time to happen. Make sure among getting the ending credits, do not turn off the game. You have to access a particular story book icon to end chapter 5 to start the epilogue section.
When this happens depending on your decisions will give you one of two achievements. Another way to know which ending you're getting is a picture for those respective endings. Otherwise, regardless how you choose to play this story mode. This will take a couple hours to get. You can not get both endings in a single run.
Although that sucks in a way. You do maintain your weapons from the previous run. Just remember to use particular level weapons, you need to be on that level. You may face a lot of characters multiple times both story portions as well as additional ones you can do. Honestly, I hope this helps people out to getting either Libra of Souls run achievements.