In my Jira-Cloud instance I have two projects, in my Exalate connections I have set up an integration for two Github repositories; how do I determine in the sync which repositories get assigned to the appropriate Jira project? Source: Github Cloud(old community)
In exalate for github, every connection is attached to a single repository, this means that for your case you will need 2 connections. In that case, every connection can easily code the proper incoming project on the Jira side.