If you need to box the heart on the timbers, which is making the pith in the center of the beam on both ends this is how I do it.
You can do it by proper planning; you plan your last cut first. Now that sounds difficult but it really isn't.
First I load my logs with the small end or it's also called the top end of the log towards the trailer hitch or operator position. That way you can plan your cuts based on what you see from this the small end. Now to tell what size log you'll need for an 8x8, for example, take a framing square and measure across from 8" on one side to 8" on the other, diagonally and you'll see that you need an 11 3/8" diameter log. That is measuring inside the bark on the narrow end of the log. If you want your beams to be free of sap wood then inside the sap wood ring.
The next thing I do is load the log onto the sawmill. Once on the sawmill I mark the ends of the log with a lumber crayon to show a plus sign (+) with the lines crossing directly over the pith/heart of the tree, on both ends. These cross marks/hairs are your centers of the beam/log.
Now you need to level these to the table of the sawmill, and thereby leveling them to the sawblade. I do this with a framing square. Here is a shot of me doing this:
Now you see the red cross hairs and the one with the arrow on it? That is the first face we'll be sawing. The red arrow is just to remind me where face one is.
Next to the framing square is a little block of wood. This block is the offset from the frame of the sawmill to the table of the sawmill, to read the height of the pith you look at the square at the point where the top of the block is, when it's against the square. This will tell you the height of the heart/pith off the table.
You do this on both ends:
This is a shot of the big end being checked with the framing square
Now you know how high the heart/pith is off the table. Let's say that this small end is 7 1/2" off the table and because the log has a taper to it (that the small end is smaller, as most logs have a large end and a small end), and that the other big end is 9" off the table. You need to lift the small end up 1 1/2". But after you do this check the big end and make sure it doesn't tip down to 8" or so. If it does split the difference with the sawmill taper controls and level the log's heart/pith to whatever level it comes out to be.
Next, since you have the log level and having done that with the framing square you now know how high the heart/pith is off the table. In our example log we've said it is 7 1/2" so if you are going to produce an 8x8 and you want the heart/pith in the middle then the last cut on this face should only be 4" above the heart/pith or at 11 1/2". That's it don't cut any deeper or you'll be making your heart/pith off center. So set your sliding scale to finish your cuts at 11 1/2". If you're cutting one inch boards off your logs on the way to the 8x8 then put a 4 line on the sliding scale on 11 1/2" and then start cutting on any 4/4 line above 11 1/2" and finish this first face with your last cut at 11 1/2". Here is a shot of the sliding scale:
In the above picture the 4/4 scale is lined up on 11 1/2". This was just a shot to show how you can line up the sliding scale to whatever line you'd like to finish on.
After the first face is done, roll the log 90° and do the same thing again. That is level the log using the cross hair red lines and the framing square.
Here is a shot of side two lined up:
After you have lined up face two and figured your last cut on this face, and made all your cuts to the last cut spot you roll your log to face three.
On face three, no taper controls will be needed as this side has already been leveled. Now you set your sliding scale to finish at 8". Then cut boards until you're at 8". Next roll your log over to face number four and your scale is already set for 8" so don't move it and cut until your beam is done, by cutting face for down to 8".
That's it you've now got a boxed heart timber 8x8 and boards cut on the way to it.
Here is a shot of the boxed heart timber:

If you're cutting planks, like 2" stock you'll have to adjust your scale to make the cuts in the right places to do that.
If you have any questions about doing this procedure, write me and ask specific question.
Jim Rogers