Can you please check if custom component creation can address all your issues. Grouping on and off chip components, creating a integrated circuit etc. Please note that you can create off chip components as well.
To create component please refer component author guide [Help-> Documentation-> Component Author Guide] or there are some videos available as well: http://www.cypress.com/resource-types/video/psoc-creator-custom-components
Please find the image where I am able to create an IC like external component and wires are rendering properly.
I was vaguely aware of component creation, primarily as a way of creating new digital components. This does look like I could rectify some of the issues, but it is quite a heavy-weight process and I am always wary of spending all my time honing tools rather than using them! I'll probably give it a go to create a simple off-chip connection point.
However it would be a lot simpler if we could compose modules in the schematic editor simply by grouping symbols and then adding the group to the component catalog. It is hard to see why the existing grouping mechanism does not allow groups to include components from the component catalog.