Yes, there really are two ways to take the images for the stack. You can move the entire camera assembly (not changing the focus), which moves the zone of focus in the same direction as the rail moves. Or you can move the center of the focus zone without moving the camera.
Let's take your chess board with 3 pieces, it's what... 8" square. You have a piece on the A row, the D row and the H row. You want all three pieces PLUS the board to be in focus. So from zero to 8". And your camera can only put about 3" (3 rows) in sharp focus.
Shot 1 center of the focus band is the edge between A and B. So the sharp area runs from in front of the board out to maybe half of C. This means the piece on A and rows A and B are in focus, plus some of C.
Without changing the camera, you move the assembly on the rail so that Shot 2's center of the focus band is maybe 1/4 of the way into D. That means that edge between B/C and out to 3/4 of E are in focus.
Shot 3, middle F center, so front of D to back of G is sharp (do you begin to see the small overlaps that are critical to the process?)
Shot 4, between G/H is sharp, so some of F to past the edge of the board.
If you now take the in-focus parts of each of the 4 shots and blend it into one image - that's focus stacking.
You can also see why more shots aren't necessarily better. If you move the assemble 1" at a time instead of 2.5" (or so), you get multiple shots where the focus for specific areas is good. So somehow the software has to pick just one.
Now you can also automate this the other way as you said. The software actually handles the small differences in image size automatically. But it's not as simple so the results may not be as good. This what you are alluding to by "touching the piece". That basically tells the camera to center the sharp focus zone at that point. But since the camera is re-focusing, the lens moves and the area of the image is slightly different. It may only be a pixel or two larger/smaller, but it also means the edges (lines of the chess board) move and the software has to keep those aligned.
When I use my StackShot (focus rail) it automatically does the first - since I autofocus on the coin (which does an overall or average focus) and then the rail moves the pre-focused camera assembly from the point where the highest detail is in the sharp zone to the point where the lowest area (field) is in the sharp zone.
Helicon lets you cheat by highlighting what will actually be in focus with a blue overlay (I assume Zerene does something like this too). So you
* Auto focus
* Move the rail out until the last bits of blue fade and set one point
* Move the rail in until the last bits of blue fade and set the 2nd point
based on the distance between the points, select either a step size or # of shots (the software calculates the other) so I don't get an INSANE # of shots.
This one took a large # of shots for the reverse, because the focus had to move from the tiny bit of rim left between 7 and 9 o'clock and the flat surface revealed after the split.

But that's a special case.
Let's take your chess board with 3 pieces, it's what... 8" square. You have a piece on the A row, the D row and the H row. You want all three pieces PLUS the board to be in focus. So from zero to 8". And your camera can only put about 3" (3 rows) in sharp focus.
Shot 1 center of the focus band is the edge between A and B. So the sharp area runs from in front of the board out to maybe half of C. This means the piece on A and rows A and B are in focus, plus some of C.
Without changing the camera, you move the assembly on the rail so that Shot 2's center of the focus band is maybe 1/4 of the way into D. That means that edge between B/C and out to 3/4 of E are in focus.
Shot 3, middle F center, so front of D to back of G is sharp (do you begin to see the small overlaps that are critical to the process?)
Shot 4, between G/H is sharp, so some of F to past the edge of the board.
If you now take the in-focus parts of each of the 4 shots and blend it into one image - that's focus stacking.
You can also see why more shots aren't necessarily better. If you move the assemble 1" at a time instead of 2.5" (or so), you get multiple shots where the focus for specific areas is good. So somehow the software has to pick just one.
Now you can also automate this the other way as you said. The software actually handles the small differences in image size automatically. But it's not as simple so the results may not be as good. This what you are alluding to by "touching the piece". That basically tells the camera to center the sharp focus zone at that point. But since the camera is re-focusing, the lens moves and the area of the image is slightly different. It may only be a pixel or two larger/smaller, but it also means the edges (lines of the chess board) move and the software has to keep those aligned.
When I use my StackShot (focus rail) it automatically does the first - since I autofocus on the coin (which does an overall or average focus) and then the rail moves the pre-focused camera assembly from the point where the highest detail is in the sharp zone to the point where the lowest area (field) is in the sharp zone.
Helicon lets you cheat by highlighting what will actually be in focus with a blue overlay (I assume Zerene does something like this too). So you
* Auto focus
* Move the rail out until the last bits of blue fade and set one point
* Move the rail in until the last bits of blue fade and set the 2nd point
based on the distance between the points, select either a step size or # of shots (the software calculates the other) so I don't get an INSANE # of shots.
This one took a large # of shots for the reverse, because the focus had to move from the tiny bit of rim left between 7 and 9 o'clock and the flat surface revealed after the split.

But that's a special case.
-----Burton
Author: 3rd Edition of the Sample Slabs book, https://www.sampleslabs.info/
50+ year / Life / Emeritus ANA member (joined 12/1/1973)
Life member: Numismatics International, CONECA
Member: TNA, FtWCC, NETCC, EveryCountry (online) coin club
Owned by three cats and a wife of 40+ years (joined 1983)
Author: 3rd Edition of the Sample Slabs book, https://www.sampleslabs.info/




















