First off, this is not a post about the history of prayer beads in paganism, because the use of prayer beads is not a historically attested practice in any of the pagan traditions I am familiar with. It's about how to use them.
There are various official formats associated with the use of prayer beads in other faiths; there are many different ways to pray the Catholic rosary, for example, depending on which sort of rosary you happen to have. Buddhist or Hindu malas can also be used to keep count of various meditative or prayerful things, most notably mantras.
For pagans there aren't any similar traditional customs. This can be freeing in that you can use them in whatever way you are inspired to, but it can also be a little intimidating in the sense of "okay, what do I do with this thing now?"
Myself, I write prayers to go with my beads--but I write prayers anyway, it's something I've done for roughly as long as I've made prayer beads (going on 20 years now). If prayer composition (either writing or otherwise preparing them, or coming up with them easily off the top of your head) is something you are drawn to, then that's wonderful, but it isn't required.
The main thing the different sorts of prayer beads seem to have in common is that they are used to keep track of what you are doing, to enable you to focus on the prayer itself rather than the count. (Whether the count itself is significant will depend on you and your practice, but I find it helpful myself.) Often they are used when repeating a particular prayer or mantra; the Catholic rosary forms frequently include different beads (sizes, shapes, etc.) to be used for repeats of different prayers (the "Our Father" and "Hail Mary" for example).
Here are a few ideas:
- Take a prayer you find meaningful (one you write or one you find) and use a bead on each line or stanza. (This is how I most often use my own beads.)
- Take a (usually but not necessarily brief) prayer and repeat it on each bead.
- Use a bead each to meditate on a series of things--runes, virtues, guiding principles, etc.--that are significant to you.
- On each bead, repeat a deity's name.
- On each bead, repeat an affirming statement (such as "I am strong." or "I am present in my life.")
- On each bead, repeat a significant word (such as "Peace." "Strength." or "Release.")
- On each bead, breathe.
Finally, prayer beads don't have to be fancy or complicated in order to be useful; you can make a simple set in a matter of minutes by tying knots in a piece of string. (You can of course also make a more traditional set of beads, have one made or buy one ready-made. :))
The important thing, I think, is to have something to hold onto--for me, using prayer beads helps me to take prayer out of my head and into the physical world.