First, you must think of everything being plumb and level. You could place level marks on timbers with flat areas or areas that have been flattened. These level marks are one of your references for the timber. The level marks should be perpendicular to grain. If the timber is really windy use some winding sticks and find the happy medium, then place a level mark there. A level mark is signified with two lines with an "X" running to the corners of the two lines and the edges. Level both longitudinally and tangentially your primary pieces. Those are the ones such as your posts, rafters, ties, of course there can be exceptions.

How about an example. You want to scribe a bent with post, lowered tie, braces (of course), king post, rafters, braces.

For ease (because like it was stated you need to get someone to show you this, and again you should also get the Green Book and read that) we are going to scribe the tie to the posts.

1. Pick your posts and tie. This involves looking at the faces and deciding which faces should go where in the building.
2. Put them on bunks and look at their character (this is where the wind and other charateristics need to be noticed). Assign your level mark (perpendicular to grain). Any flat area will do. If you can't find one flatten one.
3. Chances are you are scribing because your timbers are not regular and therefore your level mark when you place your level on it is not level. At this point you want to keep your level on its mark and use shims under the timbers to level that mark. Level the level mark.
4. At this point you need to assign reference lines on your timbers down the pertinent faces. In short you are creating long lines to level. So take your torpedo level that is on your level level mark and go to each end of the timber.
5. At each end place a plumb line and level line all the way across the end grain. The french run this through the center and others do it other ways. The importance is you are establishing two planes perpendicular to each other. You have to have some mode of reference in building (especially with irregular timbers).
6. Connect each of the two corresponding points on each face and chalk.
7. Take your post and place them on whatever bunks are comfortable.
8. Arrange them by chalk lines that represent the outside faces by using the floor, or you can use the lines down your faces to measure the right span. Get them where they need to be when they are standing. Check your level mark for level and level those longitudinal face chalk lines as well.
9. Now place the tie on top of the posts in its proper placement using the chalk lines (your mode of reference) to measure height.
10. Make sure your tie is level both ways as well. This might require some more shimming.
11. Now is when you use a plumb line, pencil, sharp eyes, and dividers.
12. This is the point where words won't work.
13. Braces can be a little trickier
14. DONT BUMP ANYTHING!
15. Again, All of your reference lines and tools work on
PLUMB AND LEVEL.

It is quite possible that I left something out or something in that is debatable, but hopefully you get the idea.