Greetings @Sheronda! That’s a great question- thanks for asking it! 
Whenever I incorporate crystals into spellwork or meditation, I choose a crystal with properties that match the intention of the spell. If I’m doing a physical healing spell, for example, I might use Carnelian- a stone associated with the flesh. However, Carnelian also has properties of happiness that I might want to work into the spell too.
I’m sure anyone who has worked with crystals will find that most crystals have quite a large number of associations with them- others may disagree, but I don’t know if it’s possible to include every corresponding benefit of a stone in one meditation or spell! 
Usually I just choose aspects directly related to the overall goal of the spell or meditation (whether it is one intention or multiple related things)
For me, in order to draw on the different aspects of a crystal (healing, good luck, etc) I believe they need to be addressed or acknowledged by the witch during the spell/meditation.
In the healing spell, I would call on or invoke the healing flesh aspects of Carnelian and perhaps also the stone’s ability to bring happiness- but I’d likely not address Carnelian’s ties to creativity (as it isn’t a trait related to the current spell).
That got a little long-winded (apologies!) but basically I think it is absolutely fine to use crystals for multiple intentions (or a multi-layered intention) as long everything is related/ties together (such as a meditation for health and happiness, or healing that is both mental and physical).
Blessed meditations, Sheronda! 