The first version is just wrong. Without other modifiers, "they needed" is a simple declarative in the past tense, and doesn't fit with the first clause.
The second is grammatic, but almost certainly not what you are trying to say. "We will write various configurations later as they will be needed." In this case, "as" would be interpreted as "because". This is grammatic, but seems to be stating the obvious: we will need configurations later, so we will write them later. This is pretty generic. It is also somewhat vague about exactly when the configurations will be written. It might mean tomorrow.
I think "We will write various configurations later as they are needed." is the most likely version to be used. It suggests that the configurations will be produced in direct response to needs.