There are 2 methods you can follow.
For standard manipulation, like tossing in updates to an already built and captured WIM, you should try using DISM
The other alternative is if you need to do not only updates, but potentially change out installed software (thick image.) If that is the case, then what I do is build my initial Windows install in a VM, and get it perfect. Then shut down the vm, copy it somewhere else (for backup) and sysprep/capture the new wim. Then, if you need to make changes, you have the copied one, that has not been sysprepped. Repeat. I rebuild the image completely about once every 4-8 months, just to make sure its as clean as possible.
Are you using MDT 2012? Look into it...its awesome.