For the certificate stuff, you may take a look at the as3crypto library, which is doing an awesome work in implementing various cryptographic and security related algorithms in AS3. I've used this particular library to do data signing and verification, using an external X.509 certificate.
The implementation in this library is pretty straightforward, and you shouldn't be confused about it, if you are a little familiar with cryptography and the whole keys/signing/certificates world.
[Edit] If you are not, you might want to take a look at the Digital Signature page on Wikipedia, which is a pretty good introduction to this world. Also, because the AS3 implementation of RSA is quite slow, if you want to sign a large number of data, you may want to sign hash of the data instead of the real data. For the practical code to do this kind of stuff, there is some code sample in the demo of the library.
Also, as you mention that your certificate is coming from an USB drive, you should be aware that using AIR 2.0, you might be able to monitor plugging and unplugging of mass storage devices. That might be cool for your application.