Overlays

Overlays need to know what surfaces they should appear on. When you first create an overlay, it only applies itself to the face you clicked on. If a brush gets clipped (which actually just deletes the brush and makes two new ones) or the overlay moves to another brush, it wont appear.

To assign which faces the overlay should appear on, double-click them to open the properties window and look for "Brush faces." Use the eyedropper tool to select the faces you want the overlay to appear on. Sometimes the overlay needs to be moved around a bit before it appears on the faces you've told it to appear on.

When scaling up or down overlays (and I believe moving them as well), make sure to have texture lock on (which can be turned on by pressing ).

Also be sure that the overlay is meant to be on the the certain brush face you want it. Open up the properties of the overlay, and look at the brush face numbers. Click the "select button" or what ever it's called. The face it's set to should be highlighted red, if it's not click on the face it should be on. Also make sure to have "hide mask" turned off, which can be toggled in the texture application tool.

Edit: Ninjad by ido, darn.

If the texture gets cut off when you scale up the overlay too much, that means it just spilled onto a different brush face. Add that face to the overlay (ctrl+click to select multiple) and it'll appear as normal.

Duplicating overlays does make them disappear sometimes, even if the brush face is correct. Like Idolon said, you have to move it around a little bit to make it reappear.

Duplicating overlays is tricky. The way I've found to reliably work with them:
1. Copy overlay.
2. Paste in approximately the same location as the original. (This reduces the chance that the bounding box gets messed up)
3. Manually move the new overlay to the new location.
4. Set brush faces as usual.