If you merge a sub assembly with another craft the sub assembly staging doesn't work/show up in the staging menu. This means if a launch vehicle is used as a sub assembly, then the engines, interstages, or any robotic parts do not work (even if they are manually turned on). This means that any of the aforementioned parts needs to be replaced on the sub assembly for it to function properly which can be a hassle. Hope this made sense, thanks!
This is by design. The staging for the parts in the sub-assembly are tied to the command pod(s) in the sub-assembly. This allows for creating sub-craft which can be disconnected during flight and have their own staging configuration, separate from the main craft.