If you select the board while a project is active it will be remembered for the project

By default, the active project is determined from the code that is open in the code editor. (It's possible to be editing the code of project A while Project B is selected in the solution explorer so don't be confused by that)

If you have never selected a board for a project then it works like the arduino ide where the last used board is selected.

The programmer is not currently per project but we will try to add that for the next release. It might help to show the Micro programmer tool bar so that changing programmer is easier and more obvious.

Hope this makes sense