Just attach your 3" nozzle to bottom head and forgot 90 deg elbow and the hole in support skirt when doing calculations with Compress. You may analyse elbow and hole in support skirt by hand if you find it reasonable.
I recommend you not to model your vessel with compress but just make required code calculations with it. Of course this leads you to new problems (compress calculates weight of the vessel wrong in support calculations if you don't add equivalent external load. And that leads you again another problems like false UG-22(c) marking on settings summary), but this kinds of problems are common in software that are made too automatic. You just need to know what compress calculates right and make rest of your calculations and analysis by hand.