For Yes-Man you can ignore the BoS. NCR there is an option to ally with the BoS if the elder isn't replaced.
The other two paths want the BoS dead with no other options open.
If you have saved the president while working for NCR, and have already allied with BoS, you can still do the YesMan path.
YesMan is quite horrified to learn BoS have agreed to fight alongside the NCR.
hmy:
"Great! A city run by robots - with technology that they don't control."
He then sarcastically says how they'll rest eventually, once he's dead...
But BoS will not appear in that ending and aren't mentioned again until the slideshow.
Pretty funny though - it's the first time you'll ever see YesMan actually seem worried by something, heheh.
Regards