You should read the MiWi Demo Kit User's Guide. You will need at least two MiWi boards. They are designed to be standalone devices. They have an on-board PIC18F46J50 micro-controller that interfaces with the MiWi RF transceiver module. The MiWi boards come with a demo program that you can use to set up a network using the switches and LCD as a user interface.
You can use the PICKit 3 to modify, run, and debug the code on the PIC micro.
If you change the code on the PIC micro, you can use the S.A.P. interface to send and receive data from a Raspberry Pi to the board. You have a choice of USART, SPI, or I2C. So with a little wiring and coding, you should be able to use the MiWi boards to communicate between Raspberry Pis.
Update 1
You asked about using the PICKit 3 with your Raspberry Pi. The PICKit 3 is designed to work with the MPLAB X IDE, which is only available for Intel architecture. See this question on the Microchp forum.
Update 2
In the comments, you asked how to wire the Raspberry Pi to the MiWi board. The S.A.P. pins are shown on the J1 header in the schematic from the MiWi Demo Kit User's Guide:

For a USART connection, make the following connections:
+------+------+
| MiWi | RPi |
+------+------+
| TX | RXD |
| RX | TXD |
| GND | GND |
+------+------+
For an I2C connection, make the following connections:
+------+------+
| MiWi | RPi |
+------+------+
| SDA | SDA |
| SCL | SCL |
| GND | GND |
+------+------+
For a SPI connection, make the following connections:
+--------+------------+
| MiWi | RPi |
+--------+------------+
| SDI | MOSI |
| SDO | MISO |
| SCK | SCLK |
| CS | CE0 or CE1 |
| GND | GND |
+--------+------------+