Add the spot color you want to the swatches. Delete the swatch you want
to replace it with.
You'll be prompted to choose a replacement. Choose the pantone color.
There isn't a way to directly convert. You can get all of the colors in a document into the swatches panel via Add Unnamed Colors. From there you can edit document colors to use only the 2 spot colors. And you would have to open any placed images and convert them to Duotone or Monotone
Implied with both Bob and Rob's responses is the assumption that you are disciplined enough to define swatches for all the colors you explicitly use in a document. InDesign doesn't require that you define all colors with swatches just like InDesign doesn't require use of paragraph, character, table, cell, and object styles. Good design discipline does pay off however when you need to do color substitutions, either with spot colors or even other process colors.