Serious Injuries like these are like skills (bad skills!) that are applied in addition to the normal profile. Note them down in the field for serious injuries but leave your profile as normal (maybe make a -1 below the relevant stat value).
So for as long as the Condemned has the variable Toughness of D6 you leave the "D6" in the T field and write a small -1 below. So each time you randomly determine the variable Toughness you roll a D6 and then apply the -1. Once you get the Toughness to be a permanent (let's say 5), then you write a 5 in the field and leave the -1 below.
This is the same as for normal models. Keep the stat value and apply the modificator in addition. This is important because a human e.g. can increase his Toughness once to 4. With a Chest Wound he will then have 4 -1. If you applied the wound immediately you would erase the 4, write down a 3 and wait for your next Toughness increase. This is, however, not possible as you cannot compensate a Serious Injury with a stat increase. So, again, write it to down and apply it like a skill, ie a permanent stat modifier. This is the same for the -1 Movement and Weapon Skill injuries.