Perhaps the best policy is to never log as cross country any flight less than 50 nm. This doesn't mean that you must land at a point 50 nm distance away, but the flight must be to a point at least 50 miles from the point of departure. For the purposes of logging cross country time toward your ATP, you may land at the departure point, or any point inbetween. You need only fly to a point at least 50 nm from the place from which you depart.
You needn't add or subtract; it's cross country time. If you're using cross country time for any other certificate or rating, it must include a landing at least 50 nm from the point of departure. In such a case, you may wish to specify which flights are used to meet the experience requirements for that particular certificate or rating, but I would do so only at the request of the examiner. Otherwise, it's probably easiest and most convenient to log all your cross country flights simply as "cross country."
Once you have achieved all your cross country experience to meet the requirements for the ATP, then you will have also met the requirements for FAR 135, and you needn't worry much about how you log it, as you don't need any additional cross country for any further certificates, ratings, or privileges.
The definition for cross country you need will be found in FAR 61.1(b)(3). Consult (i) for general cross country definition, and (iv) for that applying to the ATP. If anyone ever questions you, it's written very clearly and unmistakably in FAR 61, which defines the requirements for each certificate and rating, as well as the logging of flight time (61.51).
While your past logging practice has been technically correct, the generally accepted definition of cross country means that the flight must be at least 50 nm. (While a flight two miles away is techically a cross country under 61.1(b)(3)(i), most folks won't see it that way, and it doesn't look very good). On the other hand, the Grand Canyon example may cover several hundred miles of ground track during the course of the flight, and is without question a cross country flight.
You are also correct that for the purposes of FAR 61.159(a)(1), your cross country flights used for the ATP must be at least 50 miles in length. How you add or subtract, or highlight, or otherwise divide that time is up to you. However, you must be able to demonstrate compliance with the FAR by meeting that minimum experience requirement. Chances are that when you arrive to take the practical test, your logs will be given a very cursory exam and you'll go right into the practical test without question. However...
If your logbooks include a wide compilation of different time logging techniques, I recommend one of two courses of action:
The first is to provide a reference sheet detailing the dates of each flight used to meet the experience requirements for the ATP. If you have a mix of flights meeting various logging requirements and all of them can't be used, make it as simple as possible for the examiner. When you arrive, have a list of each flight by date that is used to meet the requirements of the FAR. In this way, if the examiner so desires (he or she won't), the various entries may be quickly referenced for verification.
The second recommendation would be my personal recommendation. Modify your logbooks. While any flight less than 50 nm can be logged as cross country time, the only possible advantage for you in so doing is to build up enough time to qualify for the PIC requirements under FAR 135.243. As you are preparing for the ATP with it's requirements for 500 hours of cross country time, you will already meet the IFR 135 requirements specified under 135.243(c)(2), and there is no need to have any more logged.
(It's a mute point for 121 ops, because to act as PIC, you must have an ATP anyway).
What it boils down to is that by having the experience for the ATP certificate, you negate any value in logging any flights of less than 50 nm in length, as cross country.
My recommendation then, is to include in your cross country totals, only the cross country time that is 50 nm or more in length. Log all cross country flights as cross country, if they meet the various definitions, but only include in the totals column those flights of at least 50 nm. In this manner, all your flights are logged, but only those exceeding 50 nm are expressed in the total. You can easily make a change by simply changing the total on your next page in your logbook, and making a note at the bottom of the page as to the purpose of this change. If you do, be sure to include the relevant FAR reference, and the purpose for the change.
This isn't as drastic as it might appear. You may have 800 hours of cross country time in your log, for example. You find that only 500 of them meet the experience requirements for the ATP. You simply change the total carried over onto the next page, from 800 to 500, and make a note in the margin at the bottom of the page. It need say something only as simple as "Cross country total altered to reflect only the requirements of FAR 61.1(b)(3)(iv)."
How you log the time, or display it, of course, is entirely up to you. There will certainly be others here who will disagree, and their input will be invalueable in giving you a better idea of what you may wish to do. The bottom line is that it really doesn't matter; you're logged the time legally and within the definition of the FAR, and no one can fault you are argue with you for it. How you present this information to an examiner is up to you. I suggest that you find a way to present your information in the most streamlined and simple terms available, for the sake of efficiency and peace of mind at the time of the application for the practical test.
I hope that helps.