Hi Brandon,
 
The names are done as: [set]_[trial protocol]_[trial protocol run]. The “set” just refers to all of the c3d files collected as part of one exam. So all c3d files in one zip will have the same “set”. The “trial protocol” is the row number from the TP table that was used to make the c3d file. The “trial protocol run” starts at 01 and goes up as you run the same TP more times. 
So a file name like: 03_05_07.c3d means: this is the 3rd exam of the day for the subject, row 5 from the TP table was used, and this is the 7th run of TP 5.
Cheers!
Duncan