The most common usage of impleo is with the accusative and ablative.
- The accusative tells you what is being filled.
- The ablative tells you with what it is being filled.
- N.B. By analogy with plenus + gen. (= "full of X"), sometimes the genitive is used here instead.
Impleo poculum (acc.) vino (abl.) = "I fill the cup with wine."
Augustine provides a handy usage of this in Confessions I.3:
...te toto imples omnia = "You fill all things with your whole self."
Your example quote uses the ablative, but in an entirely different way. Impleto caelo et terra is an ablative absolute with the past participle of impleo, and is syntactically separate from the rest of the sentence. Here's how you should parse it:
et quo refundis And where do you pour back
impleto caelo et terra once heaven and earth have been filled
restat ex te? remains of you?
Or, more fluidly:
And, once heaven and earth have been filled, where do you pour back what remains of you?