Andre
Jumpers are not that interesting since they tend to be used to isolate things - like the SWD from the OpenSDA circuit or for measuring processor current consumption.
And the various headers (populated or not) are mainly connections to processor pins, where the usage then depends on how the pin's are configured. A general description of the numerous possibilities is not realistic; it is best to get to know the pin MUX functions in the chip itself and then decide which ones you need to use and then on which connectors that can be found.
The RF header and the Bluetooth header are not specific to these functions because the are not really any different to the other general header connectors - eg. in the past people have used small RF modules needing 8 pins with this layout and so the board designers put the same connector footprint so that it could be reused (SPI functions are in the correct place) but is is nothing specific to the processor.
Regards
Mark
