Advice for 2 babies close in age?!

Agnes
I'm hoping for some advice from more experienced moms who had babies close in age. My daughter is 14 months old and my son is just a touch over 6 weeks. I'm still home with him, but she's with her regular nanny all day and I'm on my own to pick her up and put her to bed.  My problem is that while I'm bathing her and getting her ready for bed, I leave my son in his crib but he cries most of the time.  
I've tried bringing him into my daughter's room but he still cries, the whole bedtime process takes longer and feels interrupted and I sense that my daughter isn't thrilled with the intrusion into "our" time. I've also tried giving him his bottle right before the bedtime process, thinking he'd sleep afterwards, but that messed up his feeding schedule and ended up with him crying and throwing up ☹️
How long is it ok to leave him crying?  I keep reading how young babies can develop brain damage from the excess cortisol (stress hormone) if left to cry without attention.  Altogether, he's in his crib for about half an hour, I do check on him a few times and try to soothe him, and he stops and starts crying...I don't know if that means he's learning to self-soothe?
Just to clarify, I'm not trying an intential cry it out with him as I know he's still too young.  I'm just looking for some other ideas, or maybe just reassurance. Thanks in advance!