you can also use keyboard cursor left and right buttons or xtra mouse buttons to switch between systems in system build menu to reduce (additional) mouse clicks for example. I forgot to add the "auto-build" governor, you can activate it by going to the Empire menu, then onto Systems submenu and there clicking on a system of your choice and press 'a' on your keyboard. After that the AI takes over complete planetary management of that colony (including labor unit allocation and so on). I do that later-on in-game when I have smaller colonies I don't want to babysit. You can interact a little with it by adding things manually to the build list, that way the AI decisions are overruled until the build list is finished becomes empty again, then the AI kicks back in automatically.
I also forgot to add user-definability of this governor to the list of version 1.0 roadmap things. Right now it asseses the colony and decides for a strategy itself, without user interaction in that respect.
At the beginning, when there are no "resource allocators/distributors" (a special structure available when reaching certain tech levels, you can look the requirements up at the bote installation folder under \data\buildings\ in the buildings editor provided there), the player is required to babysit his first colonies but in this crucial phase of empire build-up, it's a good thing to do so.
The level of available automation increases as tech develops. At the beginning you are pretty much left with single resource routes (see one of my larger posts at the bottom of page 1 of this thread for some further helpful explanations regarding the use of it; they can be found in the system trade menu and can be laid just like trade routes; they represent what you want with automatic taking resources from a specific type from the colony connected to) but this is wanted since the first 50 turns, focussing on building up your small empire is pretty much everything you do in-game with next-to-no interaction with other players since you just haven't met them.
There is no need at any time however to manually transfer any resources via transport ships or global storage (the one in the system trade menu). Resource routes are nearly always sufficient since titanium is the one and only needed resource at the beginning of the game. They are however not working vice-versa or two-ways, that's probably what you experienced. If you want to have colony X gain auto-access to the storage for a specific resource at colony Y, you need to switch to colony Y and there lay a resource route (if available, check maximum number of routes) to colony X. You can switch through the type of resource by clicking on the button labelled titanium or whatever resource was last used.
Maximum number of routes can be a bit tricky to read, here's an example on how to read the info. Let's assume we just colonized a fresh new world, then we mostly have 4 bn. people living there (with later-on colony ships it increases to 8 respectively 16 bn.). Switching to system trade menu we see that there are 0 trade routes available and 1 resource route. That's the standard. You can always lay one resource route "for free" so to speak. Every additional resource route from that system goes at the cost of one trade route, so if you have a colony with 25 bn. people currently living there, you would normally be able to set 1 trade route and 1 resource route, 2 routes in total. If you don't have trade partners, you can set 2 resource routes but won't be able to set a trade route until you cancelled one of the 2 resource routes. Cancelling trade routes btw. works the same as setting one. You'll notice the line on galaxy map becomes pink, this means the route is going to get cancelled within the next 5 turns.
One exception to the no-manual-transport-need-rule is the deritium resource. It is scarcely available and you will probably get into the situation at some point where you have a colony with large industries but lacking its own deritium deposits. When reaching tech 5, there is a deritium allocator so you won't have any trouble from that on. But before tech level 5, you actually need to build one or two transporters and manually ship around deritium. It has gameplay reasons. For deritium being very precious it should be a somewhat dangerous thing at the beginning to work with and a potentially interesting target for enemy intercepting fleets to target these transporters and do a lot of damage.
On a side note, there's a buildings editor included where you can mod a lot of things, also for example cut out resources and resource costs thus greatly reducing the amount of micromanagement needed for the game. You'll surely get into some game balance issues but nothing a good modder can't handle. Also there's the possibility to increase outputs or just changing required tech levels if you don't want deritium troubles at all in-game.
dragonfk: Microprose's BotF was sadly heavily bugged so it is highly likely it won't run on nowaday machines. There is however an active modding community at
www.armadafleetcommand.com/botf with a lot of nice mods.