My bet (or hope) is that items stack with each-other still, even if they're of differing quality. Maybe when you hover over a stack of items in a slot, it'll show how many of each quality you have, and you can select/split specifically?
Though, inventory size is supposed to be further increased by higher-quality modular armours, which may also help...

Ratios will be fine if you simply don't use quality modules in that specific build. Quality in = quality out.