It is helpful to think of a cabochon or stone in terms used to describe a cut gemstone.
The easiest cabochon to bezel set when first starting is one without a lot of angles, corners, and curves. Round and oval cabochons are good. Cabochons can be thick or thin-first photo. They do not always have to be gemstones. Glass pebbles-second photo-can be made into a beautiful piece of jewelry.
These have one thing in common. It is easy to find where the stones start to curve in above the girdle. The bezel should be at least 1mm to 1.5mm higher than that point. The larger the stone, the wider/higher the bezel may need to be to hold it in place. Half a millimeter can make a huge difference in how much of a stone top is covered with a finished bezel as well as how it looks.
The crackle fire agate on the left in the first photo needs a wider bezel than the amazonite cabochon to the right. If the same height bezel wire used on the crackle fire agate was used on the amazonite, it would be very difficult to push the top edge of the bezel in smoothly without kinks or overlaps around the edge. After bezel setting a few stones, you will get a feel for the width of bezel needed for cabochons.
Since I live by a lake and collect stones to set, I am using a sketch of them to describe where to measure for bezel width. The bezel wire must be wide enough to cover the girdle-the dotted line on the stones-and to cover a bit of the crown-the crown and table by a millimeter or more.
The arrows on the rocks show how high the bezel wire must at least be to capture the stone. In most cases, the height of the girdle around the rock will not be the same. Most of the time this will not be a problem, as in the first rock. If one end of the rock is too thin, it can be raised in the bezel with a small shim of metal soldered to the backplate.
The girdle on both ends of this rock are the same height. Viewing from another angle, the girdles on each side of the rock are much higher than the girdle on either ends. The bezel wire needs to be wider to accommodate the side girdle height, the higher of the two.
With rocks, after the bezel wire is pushed in around the stone, it is not usually a problem if the width of bezel pushed in is uneven around the stone, but some people may find it visually displeasing. When first starting out, try to steer clear of uneven cabochons and stones. If you really want to try your hand at something like uneven height stones, practice with 26 gauge copper bezel wire before working up to silver.
In most cases, glue is not used when bezel setting cabochons, but stones are another matter. Leveling stones is not new. Stones, nuggets and thin cabochons in early turquoise jewelry were set with cushions of sawdust, ground corncobs, and sometimes cardboard shims, under them which degraded over time. So long as whatever is used to shim or raise a stone is not biodegradable, it is fine to use. E6000 has only been around for a bit over 30 years, so we don't really know. A more stable alts lifespan. An alternative would be two-part epoxy. Most of the time a bit of wire shim soldered to the backplate is all that is needed to level or raise a stone. See Step 15 for a method using wire.