Can you tell if you are over training before you have big problems like being burnt out (from running)?

This is variable: Depending on your desire and physical endurance will tell you if burning out. If always tired and lose desire to workout then you are burning out.

Over-fatigued.: If you're finding yourself very tired during the day but not sleeping well at night, and if you're chronically achy, you may be over-trained. Nobody should be training every day of the week. You need one or two days during the week to rest so your body can heal and repair and recover.