There's broadly two approaches to a risk register in JIRA. Neither of them are right or wrong, the choice depends entirely on how you want to work. (You can use a mix both if it's going to help you)
- Per project - Create a "risk" issue type and add it to projects
- Advantages: a strongly project-focussed set of risks and good visibility for the people using the project
- Disadvantages: a lot of teams don't see risks as direct items that they can deal with, so they can't be planned, estimated or included. They're usually broad things that can't really fit into a development cycle.
- Global - Create a "risk" project and log risks in there
- Advantages: everything in one place, and your users won't have them in the way of other stuff
- Disadvantages: that there's only a weak link to a project and people who aren't directly focussed on them won't pay attention to them.
In both cases, the risks can (and should!) have their own workflows and fields etc.
Finally, I would strongly recommend a look in the marketplace for risks. There's a lot of add-ons that can help, and even when the add-ons themselves might not be what you need, their vendors have some very good writeups on doing risks in general.
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