I usually use one supply stop per each big station which delivers Containers, Rocket Fuel (for ship ports) and uncharged batteries, all in one train.
What opened my eyes to this challenge with containers is that you have to consider two types of train stops (not the big stations, stops - 1 per train on bigger station):
1. where you pack resources in containers - here you need to make sure the train itself comes with exactly 5 containers per wagon (I put them in 1st wagon on their return trip from unload stop, 20 for my 1x4 trains). You don't need to replenish them, they do not get destroyed in packing process so you put some more 'buffer' containers in the loop and leave it. Just don't try to mix containers from different packing loops together, it sure is possible with logic and/or balancers but I prefer to keep it simple.
2. where you unpack resources for smelting etc - here you will lose containers. And on this stop in addition to unloading resources I also need to put 20 (5 * wagon) containers into trains to let their 'packing' stop loop keep going. So here I make a supply stop and put a chest near 1st wagon of each inbound train which gets replenished to 20 empty containers from supply, and with no limit from containers returned from unpacking. So you eventually get some buffer, but it should not clog since containers coming back from unpacking would be loaded in train first, additional containers would only be added when the empty container buffer is lower than 20.
Well, It's just the idea I came with after I returned to this mod some time ago. Like, simple rules you just need to follow on all your train stop pairs and don't overcomplicate it with logic.
To illustrate, this is what my cobalt processing station looks like (cobalt ore is not here). Sorry for miniloaders, they mostly can be replaced with stack inserters
https://imgur.com/a/nZcZ63E
At the bottom is the supply stop (no rocket fuel needed here), which replenishes only containers in explosives loop, in others loops I just threw 100+ containers for buffer and left it as is. The stop at the top is for finished packed cobalt bars.
All the packing/unpacking happens outside the station, except for explosives since I don't need a lot of them and would like to keep the loop short.
About drones - I thought, maybe allow only long-range aerial drones carry them? So there would be a way to do it but with some additional resource cost per each delivery