How does one deal with a chart that has two house cusps that fall in the same sign?....how do the signs that get "left out" fit in?
This is quite a common situation. If you have two house cusps in the same sign, then elsewhere on the chart you will have signs that are intercepted - i.e lie entirely within a House and don't have any cusps at all - for example 6th House cusp at 28 degrees libra, 7th House cusp at 7 degrees Sagittarius - Scorpio is completely intercepted in the sixth.
Interpret the Houses using your normal approach. For the intercepted sign you might give its ruler by sign and House some importance, though not as important as the cusp ruler. You might also interpret on the basis that 'large' houses play a greater role than 'small' houses in the life of the person. Though you will of course need to make allowances for such things as angularity, planets in the House, aspects to ruler, etc. On average, such large houses will have more contact with other parts of the chart than the small Houses and so be both more pervasive and more complex.