Necessary to put all power planes together for 4-layer pcb?
You can put your power planes on whichever you like. 

For a 4-layer board I usually don't bother assigning a specific layer for "power planes" - I the plane layers are usually primarily ground, to ensure unbroken planes under high frequency or analog signalling. Power planes then fit in and around as necessary, ensuring plenty of decoupling capacitors of course.



If the +12V can be routed nicely on the top layer and it saves vias to do so, you might as well route it there. Assuming your plane is large enough on a single layer to provide the current you require, there is no point also routing it on an inner layer as well.

There is usually an order of precedence for signals when routing PCBs, and this also includes power planes. As you mention PCIe, the most critical part to route is the SERDES traces which must have an unbroken ground plane directly beneath or above them (i.e. no signals or power planes cutting across through the ground underneath).