What are you trying to do when you get a "lack of resources" message? Those only appear if you:
1. run out of resources due to maintenance costs
2. try to refit a ship and don't have enough resources
3. try to convert resources that you don't have to a different type
You can upgrade ships:
1. Create a design for the ship which is the same hull size (frigate, destroyer, etc.) as the old design. (An easy way is to take the original design and hit the "upgrade" button then save as a new name; this will upgrade all obviously upgradeable components - i.e. shield generator I to shield generator IV)
2. Select the ship you want to upgrade
3. Hit the button with the three green arrows making a triangle
4. Select all the ships you want to upgrade in the window that pops up
5. Hit the "retrofit" button
6. Select the new design that you created from the list.
Note that you need a spaceyard in the sector to upgrade ships. You may also want a supply depot in the sector if you are upgrading a ship's engines and it doesn't have any supply tanks, because the newly built engines won't have any supplies!