Let me see if I have this straight. When you full length sized you were getting 4 loads per case - Correct? So you thought by neck sizing only; you would get more loadings per case. This is true if you have excessive head space. The case will stretch to fill the chamber and you shrink it down and then repeat the cycle. This can cause head separations. On the other hand If you are loading extremely hot; neck sizing will not increase case life. Loading to safe levels and neck sizing should increase your reloading to 10 or more. You may have to bump back the shoulder once or twice along the way. If you do have excessive head space, only bump the shoulder back enough to chamber reliably. If you really want to do neck sizing to the point of stressing the case as little as possible - you should have a die that takes bushings. Then get a bushing size that will shrink the neck down just enough to get a grip on a bullet when seated. Using a neck sizing die; it will shrink the neck down and then when the expander ball comes back out, it will expand the neck back up. It works the necks as much as going into a full length die - it just does not move the shoulder back and shrink down the body diameter. To really do a proper job with a bushing type die, you need to turn your necks so they are all uniform in thickness and not use an expander ball. Short of that, you can choose a bushing size that will shrink it a minimum amount and then when the expander ball comes out, it will expand the neck a minimal amount. Uniform neck thickness is not as critical in this case. The neck will be shruk down and then expanded back out, but not as much as a full length sizing die or a neck die.
As far as marking you cases for orientation - yes you can mark your cases by filing a notch in the case head. There are other ways. Some just pick a letter on the case head such as a W or a R and orientate it up each time the case is chambered. I have seen the letter filled with red. Pick out a red color that will fill the bottom of the letter and not come off easily. If any gets on the top of the case it will wear off when you chamber the case or in the tumbling process, but the bottom of the letter will still hold the color. Use some think that will stick to the case well and is not too thick in nature. A drop of lay out die that die makers use is almost perfect for this purpose. You can get it in red or blue. I do not think that marking your cases for orientation is going to make much difference in your groups. Bench rest guys have been doing this for a long time, but remember they are looking at any thing that will get them a couple of .01" advantage. They go to extreme lengths to get top accuracy. They try every little trick to get better accuracy. None of which in them selves is a big deal, but you start adding up the little things, you start getting a better group. By marking you cases you are not going to get a rifle that shoots .75 MOA down to .3 MOA; it just is not going to happen. If you are having trouble with fliers, it may shrink down your groups by eliminating your fliers, if that is what is causing your fliers. If you are getting nice round groups, I do not think that case orientation is going to help you.
While I feel I am fussy about my reloading, I am not as fussy as I need to be to be a bench rest shooter. They buy the best cases they can get to start with. Then they meticulously prep them. They weigh cases so they are almost exactly the same and put them into lots by weight. They de-burr the flash hole exactly the same for each case, they uniform the priming pockets, they precision turn their case necks and some times ream necks so that they are EXACTLY the same thickness and are uniform from case to case; so they fit the under size necks of the custom chamber in their rifles just right. As mentioned already, they will turn the necks so they do not have to re-size at all, just fire and reload. The case expands just enough to release the bullet and then it shrinks back down to grip the next bullet. They trim all cases to exactly the same length - no + or - any thing. If they start out with 100 cases, chances are they will not end up with half of them for competition, even using the best cases they can get to start with. Some do much more than I have mentioned, just to gain a couple of tenths in accuracy. Most of their accuracy comes from using a top barrel, action, trigger, scope and stock. All the gyrations of the case is to gain very little, but gain it does. I feel good if I can consistently be under .5" at 100 yards with my varmint rigs -not nearly good enough for bench rest.
Sorry about going on and on - it is now 5:00 AM here and I was just bored I guess - Good Luck and Good Shooting