Draw story scenes on thin paper and mod podge to prayer stones
We have done prayer stones as well. If you don't want to go to the expense of paint pens (much easier for kids than actual paint and brushes on such small surfaces), you can have them draw with permanent marker on very thin paper, then use mod podge or diluted glue to cover the stones. We did that for a series on the Life of David. We used paint pens this month making prayer stones for Daniel. We provided a simple tutorial of a lion using one of my favorite kids' art blogs: https://artprojectsforkids.org. Kids had an option of drawing their own, using the tutorial or choosing something different to put on their stone.
Jaymie
Moderator adds: Another idea you should check out is Carol's -- Lord's Prayer -- Prayer Rock Art Lesson https://www.rotation.org/topic/295011598215940834, it also includes member adaptations, at the end of the lesson, which use permanent markers to draw on the prayer rocks.