CPU on connections
 

Is there any advantage for cpu by booking a connecting flight as two separate segments if the flight numbers are different?
(I know that if the flight numbers are the same it is a good idea to do this otherwise the upgrades will not clear unless both flights clear)

Nope. There's actually no such thing as them being booked "together" - that can only happen if they have the same flight number. The grouping you sometimes see is just a graphical overlay.