How to move baby back to sleep in crib?

Fion
The first 2-3 months we had our son sleep in the pack and play next to our bed most of the night. 
Then, when he got sick and had fever from all the vaccines, we co-sleep for a few nights as he kept on crying. After that, we have no luck putting him back to his own bed....
We tried to move him to his bed after he fall asleep in ours; however, he will either wake up crying or only sleep less than 5 mins...
We also tried cry it out the other night, he cried to the point having a hard time breathing... So we gave in. 
We would like to try again this weekend maybe with different methods?! It will be great if you can shine us some light on how we can transition him back to his bed a little easier than just let him cry?
he also has his own room with a crib too.... Which he never sleep at before ....
Thank you!