First of all, congrats on your new chins!
Can you take Pippin out and put him in a playpen or somewhere safe, and then spend some time talking to Merry while he's still in the cage? Even if he's hiding, if you stand there and talk to him softly and offer him toys or sticks, he'll get used to your voice and presence. It gives you some one on one time with him.
He's really young, I'd guess that's adding to his nervousness.
I have a bonded pair of girls who are the same way, but they're 8 years old. The shyer one gets pushed out of the way all the time, but she's also a more withdrawn personality and likes having her more dominant cagemate to reassure her. I've been told it's pretty normal to have one chin be more bossy, as long as there isn't aggression they will figure out how to get along.
Make sure Pippin is getting enough food/water - I have two water bottles, food bowls, etc.
Good luck!