Let's see....how many questions are there here?
I'll try to simplify things: Reading-CNJ passenger and freight trains between JC and Philadelphia were operated with pooled crews and power, although my recollection is that Reading power predominated on the passenger runs. Revenue was prorated by some formula, probably something other than mileage, since the CNJ had greater terminal expenses.
B&O never operated "through" freights east of Philadelphia, if by that you mean power and crews. East of Philadelphia they were Reading or CNJ freights, depending on where they were, and operated by pooled RDG-CNJ crews and, in the steam era, power. In the diesel era, B&O power usually ran through, and by the 1960s the three roads were pooling power on the JC-Potomac Yard freights, but not western traffic. However, solid B&O freights, on schedules largely set by B&O, did run through -- particularly between JC and Potomac Yard.
Although the contract arrangements varied over the years, B&O passenger trains used B&O power (both steam and diesel) all the way through and, as far as I know, were also manned exclusively by B&O crews.