While it varies state to state, if you have made bond on the FTA, then the court will likely move forward and determine whether you wish to plead guilty or no contest or fight the charge. Some courts will allow you to make a payment plan. However, there is the chance that you will be taken into custody if you cannot pay the outstanding fines, so you should arrange your affairs just in case as this varies from state to state.
If I'm reading your question correctly, you had a 1997 disorderly conduct, and you failed to appear for that. Then, this year, in 2011, you were picked-up on the FTA, and you were given a bond, and you bonded out. In this situation, you should be scheduled for arraignment, which has nothing to do with your FTA. Arraignment is simply a court hearing where the judge asks you whether you are pleading "guilty" or "not guilty" to the disorderly conduct, and the court will also see what you are doing about an attorney. In 99% of cases, a defendant pleads "not guilty" at arraignment, and they are given dates for a Pretrial hearing and for Trial. You can always change your "not guilty" plea to a "guilty" or "no contest" plea after a deal has been negotiated with the prosecutor.
Mr. Main offers a good explanation of what happens at arraignment. For sentencing purposes, this is punishable by up to 60 days jail, so it is a good idea to talk to an attorney. I practice in Pinellas county if you wish to contact me at my website numbers below.
Arraignment informs you of the charges against you and allows you to enter an initial plea. You can plead not guilty, no contest, or guilty. The maximum punishment for a second degree misdemeanor is $500 fine and up to 6 months probation or up to 60 days in jail. I would try to check with the clerk on the FTA. I would be surprised if it was still open after almost 14 years.