Hey there,
we moved our physical Kanban board to Jira Online because our team works from different locations and apart from that there are definitely other benefits of Jira.
Our workflow looks (a little bit simplified) like that: We have two Kanban boards.
- Backlog Kanban: It's like a discovery Kanban board, where we sort out requests we won't do and define the other requests until we have all the information we need to start the developements process. Most of the time the requests are Stories; while defining we often create Sub-Tasks. The Sub-Tasks are between 2h and 8h (sometimes 16h). It's a very basic board with only 3 columns without WIP Limits etc etc. You might say we are only using it to qualify the requests and produce a valid backlog.
- Task Kanban: That's our delivery Kanban system. We work on the Stories, but in fact we are pulling the Sub-Tasks through the Kanban workflow. And adjust the corresponding Stories when all subtasks have moved.
But now I encounter a problem:
We have added WIP Limits to the Task Kanban board. Since the actual packages of word the developers are working on are the Sub-Tasks (and maybe Bugs and sometimes stand-alone Tasks) we included these in the counting of WIP. But now if a Story has 3 Sub-Tasks, there 4 counts on the WIP. 1 for the Story and 3 for the Sub-Tasks.
I tried to exclude Stories and Epics from the board. Now the Stories are not counting in the WIP Limits but they are also missing when I want to use the Kanban-Backlog. 
Are there any best practices for situations like this?
What do you think?
Might we just limit Storie in Progress (SIP = WIP)? But my concern is, that our Stories are so big 