While I was using schematica also for the first time to build some IC2 stuff in my survival world, which has a bunch of upgrades (upgrade slots can't be accessed by hoppers, etc.) separated into several of my machines, I found that the material list didn't include any of them, nor did any of the items that were in hoppers and chests when I saved the schematic file. I think that items inside containers (at least those that don't drop items when you quit their GUI) should be optionally included into the material list.