I found a good time to complete the bonus levels. Let's solve them right now.
Bonus Level 1: The first one of the two and it's challenging to figure out, just be really stealthy around Sam. Don't worry, it becomes more easier towards the end.
Secret Clock requires using the Elastic gadget as a catapult at the start to launch yourself into a hole.
Bonus Level 2: Not as long or hard as the last one, just be aware of the fireballs when travelling to the past at many occasions. Yes, it's another level with the awesome Magical Chronometer.
Secret Clock has you sneak past Sam and then jumping onto a hidden platform.