There are a number of trucking specific programs that are available. Truckers Helper is popular and they have several versions that you can buy from company driver to fleet. It is a bit more complex than some prefer, but will do about anything you need as far as running and tracking a trucking business is concerned.
www.truckershelper.com . Another is Easy Trucking. I believe that they still only have two versions of the same program. The only difference is in the number of trucks you can put in the program. Although I don't care about the way you need to do some things with the program, it will do your IFTA, invoicing and print reports.
www.easytrucking.com . The one that I find is easiest to use is trucknpro. It will do your fuel and maintenance reports and do fuel calculations, but won't do your IFTA taxes at this point. I like it for the simplicity. I know a couple of my friends also have the program and it has been doing a good job for them.
www.trucknpro.com . I believe all three either have a demo you can see online or a trial version you can check out for yourself. They are always making changes to improve the program. I recently received a copy of the new version. All three of these programs offer some flexibility in the way you use them.
You may not find everything that you would like to have in a single program. You may just need to find the one that has most of what you want and then go from there.