The shadows are dangerous and you're eventually going to get hurt. When you've been hurt, click on the Condition Monitor tab. The tab shows you your current Condition Monitor penalty, your Armor Ratings, and your Damage Resistance pool; everything you need to know when attempting to resist damage without having to track it down!
If you've taken a wound, click on a box for the appropriate Condition Monitor. The Condition Monitor will fill all of the boxes up to and including the one that you've clicked on. Your Condition Monitor penalty is automatically calculated and applied to all of your Skills. Our example character Jarols has just taken a whopping 7 points of Physical damage. Here's how he looked before things got ugly:
... and after. Notice that the total Rating for his Skills has gone down by 2. Ouch.
The dark grey boxes indicate when your character has fallen unconscious. When the final box, marked with a "D", is filled in, your character is dead.
When the team medic or your good friends at DocWagon have patched you up, you can clear some of that damage off of your Condition Monitor. To get rid of the damage, click on a filled in Condition Monitor box. The Condition Monitor will clear the selected box and all of the filled boxes after it. Jarols was patched up for 5 points which leaves him with 2 boxes filled in, so he clicks on the third box to clear it and everything after it.