"To muddle your way through" is to make your way through a situation in an akwward, poorly planned or haphazard fashion. If an actor forgot his lines for a play, he might try to muddle his way through it by improvising and making up lines on the spot. You might have to muddle your way through a recipe if you didn't have the right ingredients and didn't know the appropriate cooking technique involved.
"I had planned on making a delicious chocolate cake for my daughter's birthday, but the dog ate the recipe so I had to muddle through."
"Josh forgot the steps to his dance routine and had to muddle his way through it" (by imitating his fellow dancers' movements and prancing awkwardly onstage, while at the same time praying for it to be over).
One of the many possible translations for your sentence might include:
We'd love to pretend otherwise but the truth is, we are kind of just muddling our way through. As fun as that is, we would love some guidance. = Nós adoraríamos fingir que não, mas a verdade é que nós estamos meio que improvisando / indo as trancos e barrancos / fazendo as coisas de qualquer jeito. Por mais divertido que isso possa ser, nós gostaríamos de alguma orientação.