When resources are collected such as when some asteroid ore gets processed at a refinery and refined into metal, it will no longer just vanish and get added to the resources total counter at the top of the screen. Instead the metal gets added to the colony inventory and will remain there until its used or moved to another location.
If you have seperate colonies for ore refining, equipment and ship production then you will need to transport the items they require between each of them rather than having your entire empires resources available invisibly no matter where they are being used.
All ships have at least a small cargo hold but I will also add new transport ships that can carry large volumes of cargo but will be quite fragile and defenseless.
This is how the transport orders screen currently looks. I would like to keep it as simple as possible, so I am not adding multiple waypoint settings and items will be seperated into different cargo catagories. If you really need to transport cargo both ways between planets you will need an extra transport ship with different orders although there shouldnt really be a need for this.
Something I am also experimenting with is requiring the "data" produced by research facilities on colonies to be transported back to your designated capital before the points can be spent on research projects.
Most of these changes are to discourage having well defended colonies that are isolated away from your main empire but still be fully functional.
Hopefully this should all make empire building a lot more complex and enjoyable and open up a lot of possibilities for features I would like to add in the future.
EDIT: This is all still subject to change as it may turn out to be no fun or requires too much micro-management.