Here's what the Schulz Museum says

Full-color Sunday comics have been a long tradition in newspapers. Sundays were reserved for big, multi-panel comic strips printed in bright colors and featured in their own section known as the Sunday Funnies. Though Charles M. Schulz always drew his comics in black and white, he did have a hand in choosing the colors for his Sunday strips.

Schulz sent his completed black-and-white Sunday strips to a local printing company to have a negative made. From the negative, a reproduction of the strip was made in a smaller size than the original. Schulz would hand-color this copy and have his secretary number the colors using a color chart, as shown in the example below. The newspaper syndicates used this numbering system to identify the correct color dye for the printing plates for the Sunday Funnies. Eventually, Schulz’s secretary took over the entire coloring and numbering process under his supervision.