I have a question about what the best way to create a large master assembly using routing.  I am using SW2009 SP 3.0.  I have been using routing for about 1 year now and SolidWorks for about 2.5 years.   We design commercial biodiesel plants and equipment at a variety of scales.  I have messed around with several different design styles to create the assemblies we deal with.  The way that I view the plants is much the same way that we build and assemble them.  A tank is created and it is a subassembly, the tank is made as a part with  places for flanges to mate up to, I then mate library fittings to it, however no routes are started.  From that tank I create another sub assembly which is the tank and the pump, this sub assembly will then contain the input and output manifolds/pipe routes.  This pump, manifold and tank assembly is often only one piece of the plant and must be integrated with other tank assemblies as well as the plant space or building ( which is another assembly) .  So for the entire plant my design tree is made up of multiple assemblies.  I like this  for a multiple of reasons 1) I am  able to isolate and create drawings of just what I would like to without having to create multiple display states 2)I am able to use  one tank, pump, manifold assembly file  in several different plants and universally upgrade them as needed 3)  I am able to deal with smaller files which work faster on the workstation and in SW.  However where I run into problems is that when doing this I am inevitable having to create pipe runs and routes in between these sub assembly's (liquid cant just travel on the floor it has to go through a pipe)  However SolidWorks/ routing has trouble recognizing and mating up flanges or pipe the the other sub assemblies,  I also dislike having 5-10 pipe routes in my large main assembly that make it hard to manage the drawings and make sure that pipe spools and ISO are created for every run.  The only solution to this that I have found is to do just about everything in one large assembly with very few sub assemblies,  to me that is an unacceptable workaround,  does anyone else know of other workarounds or ways to create these large plants with multiple components all integrated together.