Clients who have requested logos with multiple colors will find that each component with a different color is saved under a different keyboard character. As an example, let us take a two colored logo (a yellow sun above a green tree). The letter "A" represents the sun, and the letter "B" represents the tree. In your word processor, type out "AB". Select the letter "A" and format it to have the color yellow. Now select "B", format it to have the color green. Now select both "A" and "B", and format them to change font to your custom font. The spacing in your logo is designed such that even if you type "BA" instead of "AB", the elements of your logo will be positioned properly. If you type "AAAAA", all you are doing is stacking each element on top of the previous one. Type a space after "AB" in order to insert other characters.
For complex logos with multiple colors, you may wish to do the following. Assuming you had a five color logo with elements stored under "A", "B", "C", "D" and "E", type each letter with a space in between. Select all five letters and change the font to be your custom font. All five elements will appear separately. Select each one individually and change its color. After you have done all five, remove the spaces between the letters. All elements will move left and combine into your logo.
If you download the E-Signature sample font, you can try the above by typing the letter "ijkl". Color the "i" yellow, the "j" green, the "k" brown and the "l" blue. Now convert to the "ESignature Sample" font. You should see the following appear: