I watched the video, interesting one. I don't use auto-export myself, I don't trust the fuzzy logic behind ;-) As the Youtubers says, the vanilla code is not handling well large transports like trek. I prefer to have a more directed approaches which is more focused and deterministic.
Meaning that I'll dedicate a transport to a pair of city, and exactly a pair. The transport will only work between these two, and I'll even rename it so I know what it is ferrying between each cities. You only have to set one transport per pair and you can think of your colonies as a chain of cities, with hubs.
As for the actual 'ticking of boxes', you can indeed start with import all, there is no adverse effect in having all import boxes checked, because you'll anyway specify which good is exported and imported.
What I found a bit confusing at first is that the import checkbox is to the left of the export box, but the value to set is in the 2nd edit box, not the first, so basically, the 2 pair of controls are crossed.
Here is my capital city.
Food example .... Set to import food up to 600 and export it while retaining a minimum of 100. Import Feeder is also checked because in 99.5% of the cases, it improves things.
As you can see, there is no adverse effect in having your town both importing and exporting, because as you specify what your wagon is doing, then you don't mix up things. You can thus chain merchandises, with city A accepting food from wagon 1, but also capable of sending if further away to city B thanks to wagon 2.
Import feeder alters (among others features, but I don't use them) the import value, in that starting at 75% of the import value, the import box is deactivated. it allows only importing a good where there is a decent amount to import. Here, it will only import food if I'm at 75 or below, but not if I'm between 76 and 99. Without it, import will happen if I'm between 1 and 99 food. This allows not using up a transport slot in your wagon for a non-significant amount of good.
And now is the one and only wagon that transport good between my capital city (45 population) and my 2nd city (30 or so). Indeed, as I don't use auto-export, I have to tick boxes. But I prefer it this way, I like to know what is going on exactly.
You basically click the EXPORT box in this window, specifying the first city. Do the same for the IMPORT box, specifying the 2nd city. Tick ALL boxes. Then you reverse, you click again EXPORT, select the 2nd city, then IMPORT, select the first city. Then click again all boxes. And this is how you have the transport "ALL Jms-Ply 1-1", meaning it transports all goods (some time I have a 2nd wagon that send a particular good to a third town), between Jamestown and Plymouth and 1-1 means this is the first of one wagon doing that, so 1-1.
As I'm a control freak, I use profusely the excellent ALT-S shortcut, existing in Civ IV (and abandoned in Civ V it seems). i.e you strike ALT-S, then click on a tile, and you get a dialog box, where you can imput a label.
Here you see there are 3 labels around Salem.
Rum > PLY indicates Rum production going to Plymouth.
Ox:Beer > JMS (stone) indicates an ox (an unusual transport for me) export Beer to Jamestown and in return import Stone.
V is my way of saying the garrison has 5 units, as I'm filling up cities before a big Indian war (I have modded the game so that an Indian only costs 15 food and not 50, meaning a typical Indian tribes fields around 150 Indians units .... you better be prepared!)
And that's it. Hopes it helps a little. Clearly my way of doing is not as easy or rapid as what the person in the video does, but I like to get a complete understanding of what is going on.