You always add or substract your skill level, the specialisation, your equipment bonus and the challenge level to get your Total Proficiency (TP) for that skill roll. Let's assume you have a new character with an Adventuring skill of 35%, a Climbing specialisation (+5%) and 'Normal' Adventuring Gear (+5%). Now the character needs to climb a wet clifface with little handholds, which poses a 'Serious' Challenge (-10%). To get your TP you add together the Adventuring Skill Level, the Climbing Specialisation and the Adventuring Gear, but substract the Challenge Level: 35% (Skill) + 5% (Specialisation) + 5% (Normal Gear) - 10% (Serious Challenge) = 35% TP, which is the number you need to roll below to succeed. So that would be a very challenging thing to pull off for a newbie. (Which is why low level challenges actually add a bonus to your roll, instead of substracting).
I hope this helps! It sounds more complicated than it actually is. After an hour or so it starts becoming second nature, since all the percentages are multiples of 5.
I haven't included an example of play or sample character because I created the system for the One Page RPG Jam. So everything had to fit on a double page, except for the cover and character sheet. I'm hoping to expand on the system, then I will include examples for sure!
If you happen to play, please contact me again, I'd love to hear of your experience!