I am appealing against a conviction and have been offered to settle out of court if I do will I get my money back I've paid for appeal with and will I have won
. This should have been a civil matter in the beginning. I owe a weeks hire for a car they then reported stolen

No, the money you paid to the courts would be fees for the court, if you paid a bondsman, that is just their fee.
So not sure what fees you paid to say if you get any back.

But that is why your settlement should be enough to cover all of your costs

First, You don't "settle" a conviction in a criminal case. If you are appealing a conviction, the prosecutor may offer you a sentencing accommodation to reduce or eliminate your jail time. It may even be possible for the court to overturn your conviction in return for a plea to a lesser charge. But I have never heard of a settlement in a criminal case.

Maybe if you explain the details of this so-called settlement we can understand better.

If you feel you can prove this was a case of malicious prosecution you can turn around a sue the person who reported the car stolen.