For stationary subjects, the most reliable method is to use a tripod and a focusing rail. A rail lets you make very small, controlled focus changes between frames, which helps ensure good overlap in sharp areas.

For moving subjects like insects, perfect spacing is much harder. In practice, you often take many frames and rely on overlap. If precise manual timing is difficult, burst mode can help while you slightly shift focus through the subject. With practice, you can also time individual shots as different parts come into focus.

In general, take more frames than you think you need, with small focus steps, rather than risking gaps in sharpness.

For post-processing, a common workflow is to align the images first, then blend the sharp regions from each frame. Popular options mentioned by users include:

• Adobe Photoshop
• Hugin tools such as align_image_stack and enfuse

So the basic best practice is: stabilize the camera and subject when possible, use small focus increments with plenty of overlap, shoot extra frames, then align and blend the stack in software.