Is it OK to have the intake and exhaust pipes in separate locations for a 95% efficient furnace?
Example- the intake/combustion pipe located on the side of the house and the exhaust/vent out the roof top.
Should both the combustion air intake and exhaust pipe be located in the same atmospheric pressure zone or does this apply to the above?
I am installing two Goodman GMVC95 units
Also should I be concerned about the exhaust gas entering through a ridge vent or bath exhaust.How close can the exhaust pipe be to these.

It isn't recommended, but rarely presents a functional issue (unless there is high wind). Consult the installation instructions for required clearances regarding the vent terminations and roofline.

Agree with KC13 on this issue. The manufacturers spend much time and money on there design of exhaust and fresh air intake systems. The instruction manual lists all approved methods.