To add to this excellent advice: I would recommend having a 'workspace' for modules in the master file. Basically somewhere to the side of the main model. Save the modules by using marquee tool around these elements.
This 'forces' you to keep making new attributes in the master file, as long as they're part of modules.
What sort of things are you wanting to quality check ?
I have managed to set up a few properties and graphic overrides that review walls for things like required fire and acoustic ratings and then highlight if it has been achieved or not, as well as checking windows to see if they are in a fire rated wall and return a fire rating automatically to these, but can also be used as a check.
With regards to your layer problem, if you put the elements you want to be able to turn off and on on separate layer within your module file you should be able to manage these as normal from your master file.
As long as the module master layer is showing then the layers within the module are able to be turned on and off just like the rest. I presume you are importing an IFC in to the Archicad module and putting all elements on to a single layer. If you set your translator up to put particular elements you want to control in views on different layers then you will be able to control when and where they show up.
The beauty of modules is that you can manage the display of layers across the whole project. Just a case of working out what it is you need to achieve and then setting up your layers and layer combinations to suit.