@CommandoBob - Hi!
1) This is NOT the place for this question - the section that discusses game mechanics (movement) would be a better place, but no worries! I won't hold it against you, lol!
2) I'll tell you what I do to keep up with ship-chaining. I number my unit carrying ships. For example, I number galleons GA01, GA02 etc. If GA01 is sitting out in the ocean and has not moved, then I know that GA01 is the ship to load for maximum movement points when I bring in GA02. By being aware of which numbers are sitting and which are moving in, you can all ways use the correct ships in a massive ship chain move, no matter the stack size. Just jot down the numbers or commit the stack to memory.
3) A neat part of this is keeping up with your oldest ship that upgrades. Let's say you number a Galley GY01, GY02 etc., 'GY' for 'Galley'. It up grades over time, keeping the same designation letters. By the time it becomes a Transport ('TR' when built new, but still 'GY' if upgraded from game start), you'll know what your oldest gametime ships are, lol. This trick can also work for ground units that you start the game with - it's like a mini-game to see where your 1st worker, spear or warrior unit ends up in year 2000 after numerous upgrades (assuming you've not lost them, lol).
Of course, I think that movement is one of the lousiest aspects of the game, so I use custom settings to increase my movements from 1-3 per turn(whatever it is) to 2-16 per turn. In 2 years (the smallest turn in a normal generic campaign), ships should be able to cross an ocean if they were capable of doing so in history, in my humble opinion. Galleons, for example, crossed the Atlantic in a matter of months - both ways with luck! Of course, Civ movement in general does not cover the historic reality of just how fast even ancient man could cross land or water. They cite game balance, I say nonsense, the designers should have gone in to the design from the start with realistic movement in mind.
You however, will have to decide for yourself just how fast you want your units to be. Just don't forget to change the movement numbers in your civpedia if you decide to go mad with it like I do in my private scenarios, lol!
Happy playtime!