In the Tips & Tricks section of the Wiki Page, it details how to decode a ton of pcap files. It states that you need to create only one Case and One Session under that case.

After this is setup and the files are decoded, is it possible to add another session on XI to decode another large directory of pcap files? We have two projects we are working on and would like to keep the sessions seperate.

I didn't want to try it without asking because I've already decoded a lot of data and don't want to start over.

Yes. The system was conceived and designed with features that you request.

For each "case" the XI creates a directroy like: /opt/xplico/pol_X
For each session inside the "case" the XI creates a directory like this: /opt/xplico/pol_X/sol_Y
For each session you can copy your pcap files in the directory: /opt/xplico/pol_X/sol_Y/new/

Obviously the session and the case must be created with the XI.

Ciao and Enjoy .
Gianluca