By design, if you have multiple Bamboo Agents, then Jobs can run across any of them. The way the Stages and Jobs work are that say you have a Stage1 containg Job1, Job2, and Job3. Assuming you have 3 agents, then Job1, Job2, and Job3 can run at the same time, since by design all jobs inside a single stage can run simultaneously. Stages execute sequentially, so if you only want one agent executing at a time, move each job to a separate stage.
If you want to tie all the jobs in a single stage to a specific Agent, then for that agent define a custom capability for the agent (go to Admin > Agents > click the agent, click Add Capability) such as "agent-id" with a value of "01" of any other key=value definition. Then in each Job, go to the Requirements tab and you can add the "agent-id"="01" as a Requirements to EACH JOB, that way even though you may have 3 local agents available to run Job1, Job2, Job3 in parallel if they are all in STage1, they cannot run in parallel since only agent 1 has the custom capability.
maybe you should give us a little bit more information. Which Atlassian application ? Jira ? What do you mean with agent ? Customers ? Users ? What do you mean with stage ? At least you should mention the application with a label.
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