It's a bit confusing, but here it goes. I'm using two different phrases here. Unit design = the template you design in the unit designer. Unit = a trained unit that is using an unit design.
Step ONE
When you are designing a unit, make sure that you select the Upgradeable option. It is the last one, with a green arrow pointing upwards. In this picture http://imgur.com/AbKz9 I have selected the option to later upgrade my shield.
Step TWO
Train a unit with the unit design.
Step THREE
Research a new type of shield. I researched standing army, so I got access to wooden shields.
Step FOUR
Select the unit that you previously trained. It will now have a new option in its action menu. It looks like this: http://imgur.com/9UJl0
ALSO NOTE
When you are selecting the Upgradeable option when designing a unit, it also means that the unit design itself will automatically upgrade as new stuff becomes available. So, in the picture above of the unit design, I had no shield, but selected that I wanted the upgradeable option. However, now that I have a shield, the unit design has automatically become updated and has a shield. This will continue as I gain even more powerful shield options. Units trained with this unit design will always be trained with the best currently available shield. Such a trained unit can also be upgraded like in Step Four if better shields become available.
The pre-designed unit designs that become available often already have the "upgradeable option". Therefore, the "archer" unit will always appear as having the latest bow when trained. It also means that these units can later be upgraded as well.
