The patient's current problems always appear in the Problems tab.
When you add a problem, you will most often use the Frequent Problems list (each provider has one).
If the problem isn't in the Frequent list, you can refer to the full list. This is initially populated from the complete ICD-9 list, but you can add to it.
Having chosen the problem, it appears in the patient's problem list.
When you are writing up your note, the template can have a specialized problem list, appropriate to the type of note. When you click one of these, the problem goes into the patient's problem list, just as above.