When the recipe calls for adding jello,is this just for replacing pectin and what flavor jello should you add?
I wouldn't use Jell-o for jelly because it is animal protein, while pectin is fruit from citrus or apples. According to my notes, all animal products should be pressure canned, not boiling water bath canned, and you can't successfully pressure can jelly.
Think about this: they use gelatin in labs to grow bacteria cultures because it is so friendly to bacteria.
Where are you getting your recipes?
There are a few jelly recipes around (NCHFP has one) that call for Jell-O but they generally get poor reviews for both quality and taste. But yes, it is a substitute for pectin.
The NCHFP recipes call for Strawberry Jell-O but I suppose you can use any flavor you want.
Here is a link that might be useful: Jelly with Jello