.  If you can afford it, there are all kinds of new
scribes out there that will take all the guess work out
of the equation.  Main thing when you use the scribe
to transfer the top shape of the lower log onto the
lower part of the top log is to make sure the scribe is
held level.  The scribe opening will determine the dept
of the notch so be sure the small log end can be
notched to that dept without structural compromises.  
The logs are alternated from butt end to top end as
they are put up.  Another thing to consider is that the
logs need to be fairly level as they go up or they may
not look right and weight distribution may be
Once the doors and window openings are cut out,
they are reinforced with vertical 2x4's to ensure
they don't move out of place.  Again using a plumb
line or a level, mark a center line with a chalk line
or draw it out.  Measure half the thickness of the
rough lumber or 2x4 on each side of the line. Use a
permanent marker and mark the dept you need to
saw out on your chain saw bar.  Cut both lines as
straight as you can at a 90 degree angle to the end
of the logs.  Next clean out the cavity by cutting
the waste wood at an angle until the 2x4 fit inside
of it with enough wiggle room for natural
expansions and contractions that occur in wood.  
Be sure the bottom and top logs which serve as an
anchor for the 2x4s are also carved out; the 2x4s
must extend several inches inside these logs to
work properly.
As you can see from the
previous picture, I had
determined that pillar
foundation was not adequate
enough for this project so,
using rocks from the
surrounding area I build a
continuous foundation that is
about 12 inches thick.