I’m creating stained glass pattern
designs and using a Cricut to cut
adhesive vinyl templates that stick to
the glass. I need help coloring the different sections of the design so I can visualize how the finished stained glass piece will look.
Hello @dave888 and welcome to the forum 
Which version of krita are you using and which operating system?
Initially, that sounds like a simple task that can be done using the Fill Tool with various different colours selected.
If the background colour is ‘clean’ and the stained glass pattern borders are clean and with no gaps then it should be easy.
Otherwise, some initial modification and settings adjustment may be needed.
It would be helpful to see the .jpg image you’re using to predict any possible problems.
Please upload the .jpg graphic that you are using, in a reply here and give credit to the creator and a download link if you downloaded it from the internet rather than drawing it yourself.
If you zoom in to a particular part of the pattern and upload that image in a reply here then that would also be helpful.
Krita may help you visualize your design, but IF you will later want to transfer the shapes to the plotter, make sure that you understand the workflow to export the Bezier curves once you’re done with your design. Unless someone else will create the shapes and you just propose the coloring, in that case Krita will do just fine.
For cutting, I remember using CorelDRAW to create vector files. Inkscape is the contemporary FOSS equivalent.