The Chopping Block (sort of 2 questions)

Logicians,
I regularly import big sample files from digital audio workstations (mostly the korg D1600). The file will be one long waveform with a bunch of small recordings (words, notes, etc) that I want to turn into individual samples. Sometimes I have upwards of 200 samples in a day to cut up.
Let me preface this question with the fact that I very much understand why Logic is treating the waveform cuts the way it is treating them, I just want to figure out how to do this process with that in mind.
What I would like to be able to do is label the first file something unique to it's waveform "A5-SYNTHHIT-1". Then, as I cut, I would like each individual sample to become "A5-SYNTHHIT-1.2" "A5-SYNTHHIT-1.3" etc.
What happens is: Logic, after I make each cut, relabels things just fine. The problem is, the file that it relabels contains EVERYTHING after the cut, and now when I cut again, I am just making progressively shorter and shorter files that contain everything after the cut. So instead of having 1 second samples, I have a 57 second sample, then a 56, then a 55...What I would like to learn how to do, is how to get it to update the sample in front of the cut, so that the sample before the cut only contains UP TO the cut.
This is very difficult for me to explain. Sorry!
Example: Lets say file1 looks like this
ABCDEF
I cut accordingly, hoping to solo out AB, and then CD, and then EF. I want the file to look like:
AB
CD
EF
Instead, sometimes they look like this after those 2 cuts:
AB
CDEF (this middle sample, since it was cut after B but before anything else, contains all of the following data. LOGIC doesn't update the file after I cut the EF off to just contain CD.)
EF
Now...The logic of how this process is working makes a lot of sense. I can totally understand why it would do this. I just want to learn how to do this more efficiently as opposed to having to label every individual sample.
I know this was an amateurish explanation. I hope that someone can help explain a better process.
-mike
P.S. when editing these samples, what does everyone use to efficiently line up the samples on the grid? Anchor points are super helpful, but what tool do you use to cut samples accurately? I am trying to use the marquee or scissor tool in the arrange window zoomed in and it's fairly effective but not accurate. Any ideas?

I'd really like to see an aswer to this one as well...it's terribly annoying that you can't just cut and copy in audio files without logic messing up your project.

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