each node with two instances gives you 4 instances, and that is very much active\active, or as I believe Microsoft would officially call it, a multi-instance cluster.

You will have to put the jobs into the msdb relevant to the database the job is for, so just log onto the correct database engine and create the job via SQLAgent for that instance, using the virtual SQL name.

The link I posted shows you how to manage multi instances, its just a case of adding new xml nodes for each msdb and\or file system if you are using the file system to store the packages. NAme them so you can readily identify which is which when you open SSIs via management studio.