How do I file for custody of my son whos father is in jail?

The same way you would if he was not in jail by filing a Request For Order.  There may be a petition you need to file as well if this is the first time you've been to court for this child.  The only difference is, you have to have him served in jail.  If its a state prison, you serve him through the legal office there.  If its a county, the sheriff's department usually serves him.  You'll have to check the rules on serving him from the jail's website.  Good luck!