Currently, I have one Board with 3 projects, but the work mostly relates to the same system, so we justified utilizing the board filter to include these projects. However, we have other projects we are starting and want to utilize best practices in Jira to plan multiple projects utilizing one team. Secondary question, how can we see and work with capactiy for each team member better?
Generally, a team should have a board they share for teamwork, and others to help them with reporting or organisation.
I suspect you are already have the right model here. A project can represent a team (in which case, the model is 1 team = 1 project = 1 board), but they can also represent other things that you want to collect issues together for. Could be business projects, pieces of software, departments, even request types if you want to segregate support from development or development phases. You separate these things out by whatever rules you need, but then use a board for a team to work together on them.
Capacity planning is another question. Boards can help you a bit, but there isn't a lot of capacity planning functionality in JIRA, unless you start looking at add-ons such as Portfolio
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