Hi Jian
Sorry for the delay in answering. 
1. the way to run DTIPrep is to use the same protocol within a given study. You do not want to have different protocol files in the same study, as this could significantly bias your analytical results. So, only run the command to create the default protocol only once.

2. while the default protocol is okay, it is worthwhile to change it to your needs (e.g. if you have sedated scans, you may want to turn off the motion correction). Thus, I suggest you start up the GUI of DTIPrep and use its interface to generate the default protocol, adapt it and then save it for future use in the command line executions.

3. Finally, you are right, there is currently not a way to create the default protocol only on the command line mode. Something to correct for future uses, can you create a feature request on the github/source code issue tracker?

Thanks
Martin