Nice question Kennedy, i'll give you a long answer from my experience. Like Adair I study with Boon and am a firm believer in bare rooting half or 1/3 of the root ball at a time. First off, let's clarify that with relatively young junipers I think it doesn't matter as much if you bare root the whole thing or not. I've bare rooted over 100 younger Kishu cuttings and did not lose one. Now, on the other end of the spectrum let's talk about Junipers that are collected from the mountains which are hundreds to maybe thousands of years old. When collecting up in the Sierra or Rocky Mountains you are trying to get a dense root mat or root ball that is connected to the trunk. These are often call "pocket trees" because their root systems develop in cracks and crevices in the rock. You can often get under these root masses and scoop the tree up with a dense root mass which is all matted together. When you get home, you want to put that dense root mass into pumice and tie the tree down so it does not move. You should not bare root any section at this time, just put the root mass in the box with pumice around and roots will start growing from that dense root mass.
After say 2-5 years depending, you repot the tree and you should bare root 1/2-1/3. I think that many people are not actually bare rooting when they think they are bare rooting. Bare rooting means combing out a section of the roots until you go back all the way to the trunk. This is harder than it sounds. To do this you can use and combo of - chop sticks, bent tweezers and a root hook. When you are bare rooting the section, it is causing stress to this section. No matter how careful you are the dense mat of roots is being torn or cut and you are losing a significant portion of the fine feeder roots. If you were to bare root 100% of an old collected tree, the stress would very likely may be too much. While I don't know this, it's possible that Mycorrhiza could have something to do with it as well. Maybe keeping 1/2 to 2/3 of root with Mycorrhiza helps the trees to stay healthy. If you are always leaving a section of roots untouched then that section will have an increase in mycorrhiza-but I could be wrong about this. Boon started working with a Western Juniper collector several years ago. The first year the collector delivered approx. 40 western junipers to Boon and they all died. When Boon took the boxes apart and examined the root ball, the trees were all bare rooted right after being collected. The next year Boon requested that the collector try and get as much roots as possible and not do anything more to the root ball. The next few years Boon got something like 98% to survive.
To answer your other question, it's not always extremely easy to tell exactly what roots go to what section of the trunk. However if you have one distinctive live vein, you can just bare root 1/2 to 1/3 of the roots that feed that live vein.
Sierra after removing the outside of the wood box.
Here's a pic of my hand bare rooting one of my Sierras. As you can see it's difficult to tell what roots connect to what veins.
Here's a before on another one of my Sierra's. You can see the area I previously bare rooted in good soil and black looking native soil on the right.
Same section(even though difficult to tell)-slightly diff angle after bare root. All roots are combed out now. Notice how much of the root mass is removed from combing everything out.
