How does a JR pass combine with an IC card?

Hello, I'll be travelling for the first time to Japan and I am trying to figure out the best way to get around by train. My conclusion is to combine a JR pass with an IC card (one for long travel and the other for urban travel), but how do they work together? Is there an app like the one linked to the Shinkansen and the IC cards? Would appreciate your guidance :) Many thanks!

You use the JR Pass when you can.
When you can't use the JR Pass, you use the IC card when you can.
When you can't use either, you buy old-fashioned paper tickets.

They don�ft link in any electronic way. The JR pass is a piece of paper. You use it to pass the manned gates at JR stations. And when leaving them.
Then when you get on some non jr train you go through their gates with the ic card. In some more remote areas ic card won�ft be accepted then you�fll need to buy a paper ticket.

Enjoy your trip to Japan!

They are not used together because many of the JR Passes (i.e. JR East Pass - Tohoku) can only be used by the person that was issued the pass to, and has to include the passport number, signature, etc. so you cannot give the pass to a friend to use.

IC cards in theory can be used by anyone and are not specific to an individual, so that is likely why they are not used together.