A set of options per-project may not be enough for the complexity of your project, so vMicro has a number of Customisable Advanced layers to allow you to go so much further:
To allow the standard Options to be saved off within a configuration (within a project), simply enable the "vMicro > General > Save Board Port, Programmer Per Configuration" option.
Now when you change the Configuration (defaults are Release / Debug) the options are encapsulated within them.
NOTE - We recommend you create a new configuration, and leave Release / Debug in their default state
Read more about managing the configuration options here
There are a number of options which can be set at a Project Level, by selecting the project in the solution explorer, and pressing F4.
Read more about these properties here