You would have to have a separate flow chart for the interrupt processing. Flowcharts are meant for showing flow of control, and interrupts, by their very nature, are a break in control flow.
Typically interrupts communicate with your "main" function (or other interrupts for that matter) through the use of "shared" global variables in C-based embedded systems. I think a sensible way to represent this in a flow chart is to use a dashed line between processing blocks where such "communications" impact program flow.
I would set up a finite state diagram that represents the normal states of control and the interrupt states; each state would be a block-level element that contained a flowcharty kind of diagram.
Depending on flowchart structure, it would probably make most sense to have the interrupt originate from a node/box that doesn t derive from another, since, by definition, an interrupt doesn t spring from normal software flow (unless it s a software-triggered interrupt). It might make sense to have it on a separate flow chart, or to show it with the rest of the flowchart depending on whether it might trigger behavior in the main flow of the chart.
Usually, without a tasking OS or library, the interrupts just flag a variable that then effects the flow. I think @JustJeff has it right.
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