Do I need to spawn the schedules off on a new thread?
No, rufus-scheduler does it for you.
Do I need to create a new scheduler instance for each schedule I'm going to create?
No, not at all.
Have you tried without setting a frequency (using rufus-scheduler's default frequency)?
Although you are not hitting a rufus-scheduler issue, please read: http://www.chiark.greenend.org.uk/~sgtatham/bugs.html
You are not giving any detail about your environment, it's very hard to help you.
Try to iterate from small to big. Have a small schedule thinggy work and then proceed one step after the other.