Go to your create convoys button and click it.
Turn off auto supply and/or auto resource convoy creation.
You probably want to leave auto maintain on, just watch to make sure the bug in this routine doesn't start making redundant convoys when you are raided by the enemy. A sure sign of this is if you are being raided and your available convoys count plummets. Check your convoys for duplicates and kill the ones carrying nothing.
One option you may want to consider is going into your common/defines.lua file and change the value for SUPPLY_SAME_AREA_DIST_CUTOFF from 10 to a smaller number. This function determines the minimum distance from the main supplier province a convoy can be set up, and changing the value to say 3 makes it very easy to create convoys from one home province to another.
For pre-war supply convoys it is easy. Cancel all existing supply convoys you don't like and choose either your capital if it is a port, or a port in a province adjacent to your capital as your outbound port to take advantage of all capital adjacent provinces having max throughput. This eliminates throughput issues and unneeded supply transfer cost. If those option are not available, choose a port closest to your capital. For the majors, this would mean USA Washington DC, Japan Tokyo, Italy Citavecchia, London Dover, Germany, France and Russia would depend on where the convoy was going to. Note that this may use more convoys than the shortest distance between some outbound ports and the receiving port, but the savings in daily transfer cost more than makes up for using a few extra convoys. There is no limit to the amount of supplies leaving an outbound port, only a limit to how much a port can receive.
I usually kill one and remake it immediately so that I don't leave something out of supply by mistake, but if you do you will soon see the low supply icon pop up and you can correct the error. There is one thing to remember, if a port is receiving supply it can not send out supply. A good example being the US west coast. San Diego is a great place to receive supply as a level 10 port rather than sending supply across country and paying all of those transfer costs, with Los Angeles being a great outbound port for Pacific destinations right nearby. Or you could just build a level one port in Oceanside and use it as your outbound port to eliminate one province of transfer cost.
Resource convoys are even easier, there is no limit to the amount of mineral resources that can enter or leave a port. I usually set them up at start for the safest wartime route and forget about them until war breaks out. Example, for the UK, I just set up every resource convoy running into Liverpool.
Once war breaks out it gets trickier, as you have to factor in convoy exposure. You want to try and set up your convoys to both minimize the risk of air attack and to bunch them together as much as possible to reduce the sea provinces you have to patrol. As an example, the Brits want as much as possible flowing into and from Liverpool to avoid the Channel and Western Approaches, both of which can be easily bombed. Unfortunately it is very difficult to tell the AI NOT to run convoys thru the Med, as the AI will always take the shortest distance between outbound port and destination. And you have absolutely no control over which outbound and destination ports the AI chooses for trade or lend lease convoys.
A quick note about lend lease convoys - there is a bug here. If the destination port of a lend lease convoy is captured or a province controlling a strait is captured that blocks an existing lend lease route, the convoy is not re-routed. It will just sit transferring no IC. You have to manually cancel lend lease and then go back and request it again to set up a new route that works. This usually an issue when Leningrad, Copenhagen, Gibraltar, or Suez falls.
One advantage of manual resource convoys is that you can choose not to run a convoy from a colony or island. A perfect example of this is the island of Nauru. The AI will insist on using 33 convoys to run 1 rare a day from Nauru back to England, running this convoys thru very dangerous areas the UK can't cover. As a player, just say no. You do not lose the mineral production, it will pile up until such time as you create a resource convoy.
One time runs - on that note, you as a player can just let mineral resources pile up overseas, then once a month or so run a convoy home to deliver the goods to your stockpile, then kill the convoy till next month. This will greatly reduce your exposure.
Supply manipulation - now we come to the nitty gritty, dealing with overseas supplies. Every non-contiguous to your capital area is consider "overseas" and will have it's own depot. This can be as small as a single hex island or as large an area as several land connected continents. The larger the area overseas, the more difficult it is to supply. An overseas supply depot is treated by the AI just like your capital meaning that all supply to the overseas area will try to flow from the depot to where it is needed.
The first trick is to keep conquered overseas areas separated. If there are no enemy units and it is not a home or core province the enemy can not place new units there. So don't connect conquered territory just to make the map look pretty. North Africa is a perfect example. If you can avoid connecting the ports, you can have your depots at Tunis, Casablanca, and Alexandria. Connect all of that together and everything is likely to be supplied from Alexandria, which really sucks if you are fighting in Casablanca. India is another good example, in that the UK can't place new units there except via transport so if you are the Axis DON'T connect everything if you don't have to or supply for everyone might have to come from Rangoon. And NEVER connect Indochina to China or China to India by upgrading the infrastructure. You don't want to have to supply ops in India from Shanghai.
Another way to manipulate supply is to run supply into every overseas port you can. While supply will be drawn from you depot, if the needs are greater than the depot can provide the AI will send supply into other ports to head towards the depot. Once supply lands, then daily demand may draw it instead towards the front where it is needed if the supply is closer than supply sitting at the depot. The AI will try to meet the supply needs from the hex it is required at for every hex, then begin trying to pull supply from adjacent hexes all the way out to a depot/capital. By using this trick you are trying to place supply at a closer range than supply located at the depot.
And another way along this same concept is to delete your supply convoy heading into your overseas depot, and only run convoys into ports close to the front. This will eventually force supply into these ports to meet depot requirements. Once landed, unit demands should reroute the supply towards the front.
Capturing enemy overseas capitals. When you capture an enemy capital (or even an enemy province loaded with supplies and fuel), you get their supplies, fuel, and mineral stockpiles. The minerals should appear at your capital, but the supplies and fuel must crawl one province per day towards a port with a resource convoy heading back to the homeland to eventually reach your capital stockpile. You can however keep these captured goodies in the overseas area by NOT running a resource convoy back home. While you won't get any resources from the overseas area, you will keep all of those supplies/fuel there instead of back at your capital where they would then have to make the long trip back to the overseas area according to the wishes of the AI. In this case, the captured supplies and fuel will head to your depot to await transport.