One of the things Manusco talks about is the gaze of both the main characters and the audience as well. I think that this is a prominent queer aspect to the movie that continues throughout its entirety.
Because they can only act on their feelings when they are in private, much of the interaction between Jack and Ennis relies on thier eye contact, or lack thereof. From their first encounter, things are a bit awkward. Ennis barely looks at Jack when they're waiting for the boss to show up at the trailer. It gave me the impression that they already knew something was going to happen, and Ennis was just trying to prolong the inevitable. Meanwhile, Jack is taking sneak peaks at Ennis through his car mirror.
There are also scenes, like when one is naked and taking a bath, and you can tell of the internal struggle of the other to look or not to look. And if he does look, what does that mean? And if he doesn't look, is it because he's forcing himself not to?
The audience is also put in this position at the same time. A viewer might be forced to confront his or her own homophobic thoughts and then ask, "Do I enjoy watching this movie? Is this scene making me uncomfortable? Why or why not?" And we are also put in to the movie as viewers through the eyes of the boss and through the eyes of Alma. They give a negative view of the relationship, but for different reasons. Alma isn't so much disgusted by the queerness of their relationship, but just by the fact that she is being cheated on by someone she clearly loves. The boss, on the other hand, is rather homophobic.