I was asked by a couple friends to monogram some Toms, and while it's a little intricate, it actually wasn't as difficult as I originally imagined.
What you'll need is:
1. A printed monogram that fits the size of your shoe
2. A thumbtack
3. A thin paintbrush (think eyeliner brush)
4. Acrylic paint in the color of your choice
Then all you have to do is:
1. Using the thumbtack, poke holes through the monogram
2. Taking the paintbrush, dot the paint of your choice through the holes onto the shoe
3. Remove the paper and connect the dots!
I haven't yet found the best acrylic sealer to apply to these, but unless you wear these in heavy rain, they will be fine. The ones above are unsealed.
These were sealed with a spray-on, acrylic sealer, and as you can see, there was some bleeding and a bit of a gray-cast that came along with it. Therefore, I would recommend no sealer rather than a spray-on kind. If you still prefer a sealer, definitely check out your local crafts store (Michael's, AC Moore, etc.), but test out the sealer before you commit it to your finished shoe (mine took about 45 minutes each to finish).
Of course, if you don't have Toms or don't want to purchase some just for this, the same trick can be applied to just about any surface--just change the size of your monogram (or other stencil) before printing to suit your surface!