You can just about always make a substitution. You may not wish to make a substitution for an offering to a deity, but in normal ritual correspondence that should be fine.
Using your examples you could replace a smokey quartz with something else appropriate for the ritual. If you're using smokey quartz for its grounding properties you may want to change it out for some hematite, and if you're using it for its negativity-dispelling powers you can exchange it for jade.
You can exchange one form of an herb for another depending on its use. If you're going to use the rosemary to asperge (dip it in water and use it to sprinkle the water places) you obviously can't use ground rosemary. And if you're making a tea, potion, infusion, or other such substance you'll need to measure your herbs differently since a cup of ground herbs is essentially different from a cup of chopped herbs, and both are different from a cup of fresh herbs.