For commercially available biodiesel, you should be fine. It's WVO (waste vegitable oil) and other types of conversions where you need to modify your truck. The only thing to watch out for is your fuel filter. Biodiesel does a good job of cleaning your fuel system, so high concentrations of it may clean out some gunk that ends up in your fuel filter. I wouldn't worry about that unless you've been filling up on crappy diesel for a while though.
What blend of biodiesel are they selling? Biodiesel is rated B5, B20, and so on. The number denotes a percentage, so B5 would be 5% biodiesel and 95% regular diesel. Cummins officially approves our engines for B20. Cummins isn't saying that more than 20% will hurt anything, just that they haven't tested it to make sure it won't. Biodiesel is a better lubricant than #2 diesel, so your fuel pump and injectors are actually happier on bio than #2. I'd imagine it's just a matter of time before Cummins does the testing and says higher concentrations are OK. It wasn't too long ago that B5 was all they said was OK.
I've run B20 in my '03, and the engine seems quieter. I did notice about 1/2 to 1 mpg decrease though. Biodiesel has less slightly energy than #2, so that makes sense. The biodiesel around here is about 5-10 cents cheaper than #2, so it evens out.