One of the first things you should do is create a drawing of the frame, with dimensions. Each bent and each long wall should be drawn. Maybe even floor systems, 1st and second, and the roof planes.
Then when you decide on which numbering system you want to use, you write each timber's number on the plan on the timber so that when you have it all down and in a pile you'll still know where it goes.
There are many different numbering systems. You can use any one of them or create your own.
There are bents in your frame, that can be numbered B1=bent one, B2=bent two, etc. There are bays in your frame and the pieces that go from B1-B2 can be numbered using that type of label. Putting the B1 on the end towards bent one and the B2 towards bent two will work.
In bent one you may have several posts so they can be B1P1, B1P2, for bent one post one, and bent one post two for example.
Some people like to use letters instead, such as B1PA for bent one post "A".
Sometimes walls are lettered like wall A vs. wall B.
As long as you write it down and you understand it , it will work, if you're not the one putting it back up then you may have to teach the next person your system.

Some people look for the system that was marked on the timbers when it was erected and use that system if you can understand it.

Good Luck with your project.

Jim Rogers