When I first had to fill in on bass at a jam session, I had trouble hearing the notes on the bottom string. Everything was rolled off, so there was little high end to help find the pitch of the notes. Since then I try to use plenty of bridge pickup. It helps me distinguish things.
When I was working out the bass parts for God Bless The Child last summer, I actually worked everything out on the guitar, and then just moved it to bass. Maybe it's part of the aging ear syndrome, but it was easier that way. When I tried at first just working it out on the bass, I could tell something wasn't blending, but I could figure out what it needed.
Maybe Sir Chaunce will grace us with his presence again and we and figure out what the real problem is. So far, he's been a one-and-done.