I'm having similar problems getting my head around this functionality, so an answer from Atlassian would be terrific...here's where i've got to if it helps.
Using Shared Teams in the Plan. e.g Green Team, Blue Team. Each Team has it's own Board. The Board configuration is based on the Portfolio Team custom field. Team = "Blue" (although JIRA changes Blue to a number currently)
Within Portfolio plan, the Team is associated with the board, and if I want to push this to a particular sprint on that board, I need to override the simulation engine by selecting the sprint I want to include the work-item in (remembering that Scrum teams are supposed to pull work into a sprint so planning in this way is an agile anti-pattern)
When calculating the plan, a team is chosen by the plan calculation and shown in pale-blue colour, this makes no difference to the backlog. This is great for planning. When I have decided that I want a particular team to tackle a work-item, I either assign it to them using Portfolio by choosing the team and overriding the simulation, this shows in white in the scope in Portfolio, or I edit the issue in JIRA and because i've added the Team custom field to the edit dialog, I can choose which team to give the work to there.
Hope this helps.
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