Spot color output

Output how? Are you trying to print colour separations or are you trying to export to a format so your printer can output colour separations? If the latter, have you contacted the printer to find out what they require? How many colours do you need to separate? Did you define the swatches in InDesign as spot colours?

You can use Window > Output > Separation Preview to see how the file will separate. Process colours can he turned off so that only spot colours will show, or you can turn off all spot colours to see what, if anything, shows as process colours.