Hi! There is actually an exercise similar to what it sounds like you are painting in one of my reference texts on acrylic - here's what they recommend:
"First the canvas is stained (with a background color) - the stain is light and scrubbed on with a rag or towel, enabling you to rub it into the weave of the canvas...Scumbling the paint over the staining breaks up the surface of the city shapes, giving some depth (the background peeks through). The flat brush suits the subject, providing almost instant buildings." In this case, a stain or glaze of the background or throughout the work may help define the buildings.
I also wouldn't be too worried about overpainting something - with acrylics it is relatively easy to fix, and variations of brush size and shape will fit into those tight spaces.
I have attached a reference photo from the book as well, hopefully that also clarifies some.
Hope this helps!