This is probably so basic that your laughing, but I have brought 2 sub assemblies together in Inv 2008 in order to do a place and fit. I sketched on a surface of one of the sub assemblies and projected the desired holes needed from another sub assembly in the file. Every thing works well, but I am interested in "retro actively" changing the original reference file to represent these new holes....Like I said, I am sure that this is comically simple and I am just missing it....
Instead of projecting from one subassembly to another, I usually use derived parts to make certain that hole patterns and mating features match. Recently, I modeled an assembly that had two housings, each one filled with electronics. The two housings mate with each other (a hole pattern and a tongue-and-groove seal) and there are connectors in the housings that mate with each other. When I created the lower housing, created one sketch that located all of the mating features. When I created the upper housing, I created a derived component and imported that sketch as my initial sketch.
If you have the parts for the two housings, you can still create a sketch in the first one to locate the mating features and then import the sketch into the second one. You just need to choose your sketch origin wisely; you might choose a hole or corner that is already common to both parts.
If you do this correctly, the mating features will be associative between the two parts.
This is much easier to do if you plan from the start to make the parts mate, but you can add it later.