One of the things I do when I am adding subtle layers of meaning is that I am also attempting to sharpen the point of view. In other words, I am attempting to make the scene more personal to the point of view character, so that the reader can clearly understand whose POV.
This means thinking about what makes the character who he or she is. What words would they uniquely use, how do they view the word and how can I best translate that on to the page.
Sometimes, it can be useful to decide which words go with which character. What metaphors/similes/symbols. How does their world view and experience colour the way they see the world. A rake who loves horse racing will use different words from a civil engineer, or from a Viking. A Viking who believes in the Aesir will see different things than someone from the Christain tradition. Indeed they will see things differently from the Romano-Greek mythological tradition. Even their gestures have the potential to be different. This can be done before you begin to a certain extent, but with me, the full flowering of a character is often not evident until the first draft is done. Often little things take on significance as the story moves forward. Sometimes, I know at the start which things they will be, and sometimes I don't. And sometimes, I need to tweak them after my editor has given me her thoughts...
She felt unhappy about what had happened could describe any character in any time -- A single tear trickled down her cheek. She allowed it to linger.
'Some day I will regain my freedom,' she vowed, clenching her fists. 'I will not remain this Viken's slave forever.' describes a specific moment in a specific character's life, in this case Annis from Taken by the Viking.
There are several different exercises you can do. The most useful I have found is in Donald Maass' Writing the Break Out Novel Workbook, it involves opening your novel at random and deciding whose point of view you are in, and how you can sharpen that point of view -- either through a gesture, a thought, the timely use of a word etc. In other words, how can you make sure the scene isviewed more clearly through the POV character's eyes. This exercise is addition to the other great exercise of his for adding tension. These sorts of exercises take place in the final bits of editing for me, when I am working off screen. And yes, it does take time, but at that point I know my characters very well and it becomes fun.
First drafts for me are always hard as they are always to a certain extent writing into the mist. I may have a vague idea of where I am headed, but I do leave plenty of scope for changing and layering the subtle meanings and gestures.