If I have a misdemeanor embezzlement charge, how can I settle it out of court?

Depends on the reasonableness of your employer, but I wouldn't admit to anything in order to keep them from pursuing charges.  A classic trick of law enforcement or security gaurds is to imply that they won't pursue charges if you sign something admitting the charges.  Once you sign it,  they often hand it over to the DA's office to prosecute you.  So to answer your questions, any attempt to settle it out of court may backfire on you and you may be prosecuted anyway, so be careful if you attempt it. If you don't have a record, there's essentially no risk of going to prison with the facts you presented.